notebooks/09 - Accessing NCBIs Entrez databases.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Source of the materials**: Biopython cookbook (adapted)\n",
    "<font color='red'>Status: Draft</font>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Accessing NCBI’s Entrez databases\n",
    "\n",
    "[Entrez Guidelines](Entrez Guidelines)\n",
    "\n",
    "[EInfo: Obtaining information about the Entrez databases](#EInfo:-Obtaining-information-about-the-Entrez-databases)\n",
    "\n",
    "[ESearch: Searching the Entrez databases](#ESearch:-Searching-the-Entrez-databases)\n",
    "\n",
    "[EPost: Uploading a list of identifiers](#EPost:-Uploading-a-list-of-identifiers)\n",
    "\n",
    "[EFetch: Downloading full records from Entrez](#EFetch:-Downloading-full-records-from-Entrez)\n",
    "\n",
    "[History and WebEnv](#Using-the-history-and-WebEnv)\n",
    "\n",
    "[Specialized parsers](#Specialized-parsers)\n",
    "\n",
    "[Examples](#Examples)\n",
    "\n",
    "\n",
    "Entrez (<http://www.ncbi.nlm.nih.gov/Entrez>) is a data retrieval system\n",
    "that provides users access to NCBI’s databases such as PubMed, GenBank,\n",
    "GEO, and many others. You can access Entrez from a web browser to\n",
    "manually enter queries, or you can use Biopython’s `Bio.Entrez` module\n",
    "for programmatic access to Entrez. The latter allows you for example to\n",
    "search PubMed or download GenBank records from within a Python script.\n",
    "\n",
    "The `Bio.Entrez` module makes use of the Entrez Programming Utilities\n",
    "(also known as EUtils), consisting of eight tools that are described in\n",
    "detail on NCBI’s page at <http://www.ncbi.nlm.nih.gov/entrez/utils/>.\n",
    "Each of these tools corresponds to one Python function in the\n",
    "`Bio.Entrez` module, as described in the sections below. This module\n",
    "makes sure that the correct URL is used for the queries, and that not\n",
    "more than one request is made every three seconds, as required by NCBI.\n",
    "\n",
    "The output returned by the Entrez Programming Utilities is typically in\n",
    "XML format. To parse such output, you have several options:\n",
    "\n",
    "1.  Use `Bio.Entrez`’s parser to parse the XML output into a Python\n",
    "    object;\n",
    "\n",
    "2.  Use the DOM (Document Object Model) parser in Python’s standard\n",
    "    library;\n",
    "\n",
    "3.  Use the SAX (Simple API for XML) parser in Python’s standard\n",
    "    library;\n",
    "\n",
    "4.  Read the XML output as raw text, and parse it by string searching\n",
    "    and manipulation.\n",
    "\n",
    "For the DOM and SAX parsers, see the Python documentation. The parser in\n",
    "`Bio.Entrez` is discussed below.\n",
    "\n",
    "NCBI uses DTD (Document Type Definition) files to describe the structure\n",
    "of the information contained in XML files. Most of the DTD files used by\n",
    "NCBI are included in the Biopython distribution. The `Bio.Entrez` parser\n",
    "makes use of the DTD files when parsing an XML file returned by NCBI\n",
    "Entrez.\n",
    "\n",
    "Occasionally, you may find that the DTD file associated with a specific\n",
    "XML file is missing in the Biopython distribution. In particular, this\n",
    "may happen when NCBI updates its DTD files. If this happens,\n",
    "`Entrez.read` will show a warning message with the name and URL of the\n",
    "missing DTD file. The parser will proceed to access the missing DTD file\n",
    "through the internet, allowing the parsing of the XML file to continue.\n",
    "However, the parser is much faster if the DTD file is available locally.\n",
    "For this purpose, please download the DTD file from the URL in the\n",
    "warning message and place it in the directory\n",
    "`...site-packages/Bio/Entrez/DTDs`, containing the other DTD files. If\n",
    "you don’t have write access to this directory, you can also place the\n",
    "DTD file in `~/.biopython/Bio/Entrez/DTDs`, where `~` represents your\n",
    "home directory. Since this directory is read before the directory\n",
    "`...site-packages/Bio/Entrez/DTDs`, you can also put newer versions of\n",
    "DTD files there if the ones in `...site-packages/Bio/Entrez/DTDs` become\n",
    "outdated. Alternatively, if you installed Biopython from source, you can\n",
    "add the DTD file to the source code’s `Bio/Entrez/DTDs` directory, and\n",
    "reinstall Biopython. This will install the new DTD file in the correct\n",
    "location together with the other DTD files.\n",
    "\n",
    "The Entrez Programming Utilities can also generate output in other\n",
    "formats, such as the Fasta or GenBank file formats for sequence\n",
    "databases, or the MedLine format for the literature database, discussed\n",
    "in Section [Specialized parsers](#Specialized-parsers)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Entrez Guidelines\n",
    "\n",
    "Before using Biopython to access the NCBI’s online resources (via\n",
    "`Bio.Entrez` or some of the other modules), please read the [NCBI’s Entrez User Requirements](http://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Usage_Guidelines_and_Requiremen).\n",
    "If the NCBI finds you are abusing their systems, they can and will ban\n",
    "your access!\n",
    "\n",
    "To paraphrase:\n",
    "\n",
    "-   For any series of more than 100 requests, do this at weekends or\n",
    "    outside USA peak times. This is up to you to obey.\n",
    "\n",
    "-   Use the <http://eutils.ncbi.nlm.nih.gov> address, not the standard\n",
    "    NCBI Web address. Biopython uses this web address.\n",
    "\n",
    "-   Make no more than three requests every seconds (relaxed from at most\n",
    "    one request every three seconds in early 2009). This is\n",
    "    automatically enforced by Biopython.\n",
    "\n",
    "-   Use the optional email parameter so the NCBI can contact you if\n",
    "    there is a problem. You can either explicitly set this as a\n",
    "    parameter with each call to Entrez (e.g. include\n",
    "    <span>email=“A.N.Other@example.com”</span> in the argument list), or\n",
    "    you can set a global email address:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "<span>Bio.Entrez</span> will then use this email address with each\n",
    "call to Entrez. The <span>example.com</span> address is a reserved\n",
    "domain name specifically for documentation (RFC 2606). Please DO NOT\n",
    "use a random email – it’s better not to give an email at all. The\n",
    "email parameter will be mandatory from June 1, 2010. In case of\n",
    "excessive usage, NCBI will attempt to contact a user at the e-mail\n",
    "address provided prior to blocking access to the E-utilities.\n",
    "\n",
    "If you are using Biopython within some larger software suite, use\n",
    "the tool parameter to specify this. You can either explicitly set\n",
    "the tool name as a parameter with each call to Entrez (e.g. include\n",
    "<span>tool=“MyLocalScript”</span> in the argument list), or you can\n",
    "set a global tool name:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.tool = \"MyLocalScript\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "    The tool parameter will default to Biopython.\n",
    "\n",
    "-   For large queries, the NCBI also recommend using their session\n",
    "    history feature (the WebEnv session cookie string,\n",
    "    see Section [History and WebEnv](#Using-the-history-and-WebEnv)). This is only slightly\n",
    "    more complicated.\n",
    "\n",
    "In conclusion, be sensible with your usage levels. If you plan to\n",
    "download lots of data, consider other options. For example, if you want\n",
    "easy access to all the human genes, consider fetching each chromosome by\n",
    "FTP as a GenBank file, and importing these into your own BioSQL database\n",
    "(see Section \\[sec:BioSQL\\]).\n",
    "\n",
    "## EInfo: Obtaining information about the Entrez databases\n",
    "\n",
    "- [einfo source](http://biopython.org/DIST/docs/api/Bio.Entrez-pysrc.html#einfo)\n",
    "\n",
    "EInfo provides field index term counts, last update, and available links\n",
    "for each of NCBI’s databases. In addition, you can use EInfo to obtain a\n",
    "list of all database names accessible through the Entrez utilities. The variable `result` now contains a list of databases in XML format:\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
      "<!DOCTYPE eInfoResult PUBLIC \"-//NLM//DTD einfo 20130322//EN\" \"http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20130322/einfo.dtd\">\n",
      "<eInfoResult>\n",
      "<DbList>\n",
      "\n",
      "\t<DbName>pubmed</DbName>\n",
      "\t<DbName>protein</DbName>\n",
      "\t<DbName>nuccore</DbName>\n",
      "\t<DbName>nucleotide</DbName>\n",
      "\t<DbName>nucgss</DbName>\n",
      "\t<DbName>nucest</DbName>\n",
      "\t<DbName>structure</DbName>\n",
      "\t<DbName>genome</DbName>\n",
      "\t<DbName>annotinfo</DbName>\n",
      "\t<DbName>assembly</DbName>\n",
      "\t<DbName>bioproject</DbName>\n",
      "\t<DbName>biosample</DbName>\n",
      "\t<DbName>blastdbinfo</DbName>\n",
      "\t<DbName>books</DbName>\n",
      "\t<DbName>cdd</DbName>\n",
      "\t<DbName>clinvar</DbName>\n",
      "\t<DbName>clone</DbName>\n",
      "\t<DbName>gap</DbName>\n",
      "\t<DbName>gapplus</DbName>\n",
      "\t<DbName>grasp</DbName>\n",
      "\t<DbName>dbvar</DbName>\n",
      "\t<DbName>epigenomics</DbName>\n",
      "\t<DbName>gene</DbName>\n",
      "\t<DbName>gds</DbName>\n",
      "\t<DbName>geoprofiles</DbName>\n",
      "\t<DbName>homologene</DbName>\n",
      "\t<DbName>medgen</DbName>\n",
      "\t<DbName>mesh</DbName>\n",
      "\t<DbName>ncbisearch</DbName>\n",
      "\t<DbName>nlmcatalog</DbName>\n",
      "\t<DbName>omim</DbName>\n",
      "\t<DbName>orgtrack</DbName>\n",
      "\t<DbName>pmc</DbName>\n",
      "\t<DbName>popset</DbName>\n",
      "\t<DbName>probe</DbName>\n",
      "\t<DbName>proteinclusters</DbName>\n",
      "\t<DbName>pcassay</DbName>\n",
      "\t<DbName>biosystems</DbName>\n",
      "\t<DbName>pccompound</DbName>\n",
      "\t<DbName>pcsubstance</DbName>\n",
      "\t<DbName>pubmedhealth</DbName>\n",
      "\t<DbName>seqannot</DbName>\n",
      "\t<DbName>snp</DbName>\n",
      "\t<DbName>sra</DbName>\n",
      "\t<DbName>taxonomy</DbName>\n",
      "\t<DbName>unigene</DbName>\n",
      "\t<DbName>gencoll</DbName>\n",
      "\t<DbName>gtr</DbName>\n",
      "</DbList>\n",
      "\n",
      "</eInfoResult>\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.einfo()\n",
    "result = handle.read()\n",
    "print(result)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Since this is a fairly simple XML file, we could extract the information\n",
    "it contains simply by string searching. Using `Bio.Entrez`’s parser\n",
    "instead, we can directly parse this XML file into a Python object:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from Bio import Entrez\n",
    "handle = Entrez.einfo()\n",
    "record = Entrez.read(handle)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Now `record` is a dictionary with exactly one key:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['DbList'])"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record.keys()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The values stored in this key is the list of database names shown in the\n",
    "XML above:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['pubmed', 'protein', 'nuccore', 'nucleotide', 'nucgss', 'nucest', 'structure', 'genome', 'annotinfo', 'assembly', 'bioproject', 'biosample', 'blastdbinfo', 'books', 'cdd', 'clinvar', 'clone', 'gap', 'gapplus', 'grasp', 'dbvar', 'epigenomics', 'gene', 'gds', 'geoprofiles', 'homologene', 'medgen', 'mesh', 'ncbisearch', 'nlmcatalog', 'omim', 'orgtrack', 'pmc', 'popset', 'probe', 'proteinclusters', 'pcassay', 'biosystems', 'pccompound', 'pcsubstance', 'pubmedhealth', 'seqannot', 'snp', 'sra', 'taxonomy', 'unigene', 'gencoll', 'gtr']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"DbList\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "For each of these databases, we can use EInfo again to obtain more\n",
    "information:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'PubMed bibliographic record'"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "handle = Entrez.einfo(db=\"pubmed\")\n",
    "record = Entrez.read(handle)\n",
    "record[\"DbInfo\"][\"Description\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['LastUpdate', 'Count', 'DbName', 'Description', 'MenuName', 'FieldList', 'DbBuild', 'LinkList'])"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record['DbInfo'].keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'PubMed bibliographic record'"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "handle = Entrez.einfo(db=\"pubmed\")\n",
    "record = Entrez.read(handle)\n",
    "record[\"DbInfo\"][\"Description\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'25641704'"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"DbInfo\"][\"Count\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'2016/01/12 18:56'"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"DbInfo\"][\"LastUpdate\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Try `record[\"DbInfo\"].keys()` for other information stored in this\n",
    "record. One of the most useful is a list of possible search fields for\n",
    "use with ESearch:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ALL, All Fields, All terms from all searchable fields\n",
      "UID, UID, Unique number assigned to publication\n",
      "FILT, Filter, Limits the records\n",
      "TITL, Title, Words in title of publication\n",
      "WORD, Text Word, Free text associated with publication\n",
      "MESH, MeSH Terms, Medical Subject Headings assigned to publication\n",
      "MAJR, MeSH Major Topic, MeSH terms of major importance to publication\n",
      "AUTH, Author, Author(s) of publication\n",
      "JOUR, Journal, Journal abbreviation of publication\n",
      "AFFL, Affiliation, Author's institutional affiliation and address\n",
      "ECNO, EC/RN Number, EC number for enzyme or CAS registry number\n",
      "SUBS, Supplementary Concept, CAS chemical name or MEDLINE Substance Name\n",
      "PDAT, Date - Publication, Date of publication\n",
      "EDAT, Date - Entrez, Date publication first accessible through Entrez\n",
      "VOL, Volume, Volume number of publication\n",
      "PAGE, Pagination, Page number(s) of publication\n",
      "PTYP, Publication Type, Type of publication (e.g., review)\n",
      "LANG, Language, Language of publication\n",
      "ISS, Issue, Issue number of publication\n",
      "SUBH, MeSH Subheading, Additional specificity for MeSH term\n",
      "SI, Secondary Source ID, Cross-reference from publication to other databases\n",
      "MHDA, Date - MeSH, Date publication was indexed with MeSH terms\n",
      "TIAB, Title/Abstract, Free text associated with Abstract/Title\n",
      "OTRM, Other Term, Other terms associated with publication\n",
      "INVR, Investigator, Investigator\n",
      "COLN, Author - Corporate, Corporate Author of publication\n",
      "CNTY, Place of Publication, Country of publication\n",
      "PAPX, Pharmacological Action, MeSH pharmacological action pre-explosions\n",
      "GRNT, Grant Number, NIH Grant Numbers\n",
      "MDAT, Date - Modification, Date of last modification\n",
      "CDAT, Date - Completion, Date of completion\n",
      "PID, Publisher ID, Publisher ID\n",
      "FAUT, Author - First, First Author of publication\n",
      "FULL, Author - Full, Full Author Name(s) of publication\n",
      "FINV, Investigator - Full, Full name of investigator\n",
      "TT, Transliterated Title, Words in transliterated title of publication\n",
      "LAUT, Author - Last, Last Author of publication\n",
      "PPDT, Print Publication Date, Date of print publication\n",
      "EPDT, Electronic Publication Date, Date of Electronic publication\n",
      "LID, Location ID, ELocation ID\n",
      "CRDT, Date - Create, Date publication first accessible through Entrez\n",
      "BOOK, Book, ID of the book that contains the document\n",
      "ED, Editor, Section's Editor\n",
      "ISBN, ISBN, ISBN\n",
      "PUBN, Publisher, Publisher's name\n",
      "AUCL, Author Cluster ID, Author Cluster ID\n",
      "EID, Extended PMID, Extended PMID\n",
      "DSO, DSO, Additional text from the summary\n",
      "AUID, Author - Identifier, Author Identifier\n",
      "PS, Subject - Personal Name, Personal Name as Subject\n"
     ]
    }
   ],
   "source": [
    "for field in record[\"DbInfo\"][\"FieldList\"]:\n",
    "    print(\"%(Name)s, %(FullName)s, %(Description)s\" % field)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "That’s a long list, but indirectly this tells you that for the PubMed\n",
    "database, you can do things like `Jones[AUTH]` to search the author\n",
    "field, or `Sanger[AFFL]` to restrict to authors at the Sanger Centre.\n",
    "This can be very handy - especially if you are not so familiar with a\n",
    "particular database.\n",
    "\n",
    "ESearch: Searching the Entrez databases\n",
    "-------------------------------------\n",
    "\n",
    "To search any of these databases, we use `Bio.Entrez.esearch()`. For\n",
    "example, let’s search in PubMed for publications related to Biopython:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['24929426', '24497503', '24267035', '24194598', '23842806', '23157543', '22909249', '22399473', '21666252', '21210977', '20015970', '19811691', '19773334', '19304878', '18606172', '21585724', '16403221', '16377612', '14871861', '14630660']"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.esearch(db=\"pubmed\", term=\"biopython\")\n",
    "record = Entrez.read(handle)\n",
    "record[\"IdList\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'TranslationStack': [{'Explode': 'N', 'Term': 'biopython[All Fields]', 'Field': 'All Fields', 'Count': '21'}, 'GROUP'], 'IdList': ['24929426', '24497503', '24267035', '24194598', '23842806', '23157543', '22909249', '22399473', '21666252', '21210977', '20015970', '19811691', '19773334', '19304878', '18606172', '21585724', '16403221', '16377612', '14871861', '14630660'], 'TranslationSet': [], 'QueryTranslation': 'biopython[All Fields]', 'Count': '21', 'RetStart': '0', 'RetMax': '20'}"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "In this output, you see seven PubMed IDs (including 19304878 which is\n",
    "the PMID for the Biopython application), which can be retrieved by\n",
    "EFetch (see section [EFetch: Downloading full records from Entrez](#EFetch:-Downloading-full-records-from-Entrez)).\n",
    "\n",
    "You can also use ESearch to search GenBank. Here we’ll do a quick search\n",
    "for the *matK* gene in *Cypripedioideae* orchids (see\n",
    "Section \\[sec:entrez-einfo\\] about EInfo for one way to find out which\n",
    "fields you can search in each Entrez database):\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'334'"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "handle = Entrez.esearch(db=\"nucleotide\", term=\"Cypripedioideae[Orgn] AND matK[Gene]\")\n",
    "record = Entrez.read(handle)\n",
    "record[\"Count\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['844174433', '937957673', '694174838', '944541375', '575524123', '575524121', '575524119', '575524117', '575524115', '575524113', '575524111', '575524109', '575524107', '575524105', '575524103', '575524101', '575524099', '575524097', '575524095', '575524093']"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"IdList\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Each of the IDs (126789333, 37222967, 37222966, …) is a GenBank\n",
    "identifier. See section [EFetch: Downloading full records from Entrez](#EFetch:-Downloading-full-records-from-Entrez) for information on how to\n",
    "actually download these GenBank records.\n",
    "\n",
    "Note that instead of a species name like `Cypripedioideae[Orgn]`, you\n",
    "can restrict the search using an NCBI taxon identifier, here this would\n",
    "be `txid158330[Orgn]`. This isn’t currently documented on the ESearch\n",
    "help page - the NCBI explained this in reply to an email query. You can\n",
    "often deduce the search term formatting by playing with the Entrez web\n",
    "interface. For example, including `complete[prop]` in a genome search\n",
    "restricts to just completed genomes.\n",
    "\n",
    "As a final example, let’s get a list of computational journal titles:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0 computational Journals found\n",
      "The first 20 are\n",
      "[]\n"
     ]
    }
   ],
   "source": [
    "# nlmcatalog\n",
    "# handle = Entrez.esearch(db=\"nlmcatalog\", term=\"computational\")\n",
    "# record = Entrez.read(handle)\n",
    "# record[\"Count\"]\n",
    "handle = Entrez.esearch(db=\"nlmcatalog\", term=\"biopython[Journal]\", RetMax='20')\n",
    "record = Entrez.read(handle)\n",
    "print(\"{} computational Journals found\".format(record[\"Count\"]))\n",
    "print(\"The first 20 are\\n{}\".format(record['IdList']))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Again, we could use EFetch to obtain more information for each of these\n",
    "journal IDs.\n",
    "\n",
    "ESearch has many useful options — see the [ESearch help\n",
    "page](http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html)\n",
    "for more information.\n",
    "\n",
    "EPost: Uploading a list of identifiers\n",
    "------------------------------------\n",
    "\n",
    "EPost uploads a list of UIs for use in subsequent search strategies; see\n",
    "the [EPost help\n",
    "page](http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html)\n",
    "for more information. It is available from Biopython through the\n",
    "`Bio.Entrez.epost()` function.\n",
    "\n",
    "To give an example of when this is useful, suppose you have a long list\n",
    "of IDs you want to download using EFetch (maybe sequences, maybe\n",
    "citations – anything). When you make a request with EFetch your list of\n",
    "IDs, the database etc, are all turned into a long URL sent to the\n",
    "server. If your list of IDs is long, this URL gets long, and long URLs\n",
    "can break (e.g. some proxies don’t cope well).\n",
    "\n",
    "Instead, you can break this up into two steps, first uploading the list\n",
    "of IDs using EPost (this uses an “HTML post” internally, rather than an\n",
    "“HTML get”, getting round the long URL problem). With the history\n",
    "support, you can then refer to this long list of IDs, and download the\n",
    "associated data with EFetch.\n",
    "\n",
    "Let’s look at a simple example to see how EPost works – uploading some\n",
    "PubMed identifiers:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<?xml version=\"1.0\"?>\n",
      "<!DOCTYPE ePostResult PUBLIC \"-//NLM//DTD ePostResult, 11 May 2002//EN\" \"http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ePost_020511.dtd\">\n",
      "<ePostResult>\n",
      "\t<QueryKey>1</QueryKey>\n",
      "\t<WebEnv>NCID_1_242547791_130.14.22.215_9001_1452651583_567658845_0MetA0_S_MegaStore_F_1</WebEnv>\n",
      "</ePostResult>\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "id_list = [\"19304878\", \"18606172\", \"16403221\", \"16377612\", \"14871861\", \"14630660\"]\n",
    "print(Entrez.epost(\"pubmed\", id=\",\".join(id_list)).read())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The returned XML includes two important strings, `QueryKey` and `WebEnv`\n",
    "which together define your history session. You would extract these\n",
    "values for use with another Entrez call such as EFetch:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "id_list = [\"19304878\", \"18606172\", \"16403221\", \"16377612\", \"14871861\", \"14630660\"]\n",
    "search_results = Entrez.read(Entrez.epost(\"pubmed\", id=\",\".join(id_list)))\n",
    "webenv = search_results[\"WebEnv\"]\n",
    "query_key = search_results[\"QueryKey\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Section [History and WebEnv](#Using-the-history-and-WebEnv) shows how to use the history feature.\n",
    "\n",
    "ESummary: Retrieving summaries from primary IDs\n",
    "-----------------------------------------------\n",
    "\n",
    "ESummary retrieves document summaries from a list of primary IDs (see\n",
    "the [ESummary help\n",
    "page](http://www.ncbi.nlm.nih.gov/entrez/query/static/esummary_help.html)\n",
    "for more information). In Biopython, ESummary is available as\n",
    "`Bio.Entrez.esummary()`. Using the search result above, we can for\n",
    "example find out more about the journal with ID 30367:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Journal info\n",
      "id: 101660833\n",
      "Title: IEEE transactions on computational imaging.\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.esummary(db=\"nlmcatalog\", term=\"[journal]\", id=\"101660833\")\n",
    "record = Entrez.read(handle)\n",
    "info = record[0]['TitleMainList'][0]\n",
    "print(\"Journal info\\nid: {}\\nTitle: {}\".format(record[0][\"Id\"], info[\"Title\"]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "EFetch: Downloading full records from Entrez\n",
    "-----------------------------------------\n",
    "\n",
    "EFetch is what you use when you want to retrieve a full record from\n",
    "Entrez. This covers several possible databases, as described on the main\n",
    "[EFetch Help\n",
    "page](http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html).\n",
    "\n",
    "For most of their databases, the NCBI support several different file\n",
    "formats. Requesting a specific file format from Entrez using\n",
    "`Bio.Entrez.efetch()` requires specifying the `rettype` and/or `retmode`\n",
    "optional arguments. The different combinations are described for each\n",
    "database type on the pages linked to on [NCBI efetch\n",
    "webpage](http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html)\n",
    "(e.g.\n",
    "[literature](http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html),\n",
    "[sequences](http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html)\n",
    "and\n",
    "[taxonomy](http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchtax_help.html)).\n",
    "\n",
    "One common usage is downloading sequences in the FASTA or\n",
    "GenBank/GenPept plain text formats (which can then be parsed with\n",
    "`Bio.SeqIO`, see Sections \\[sec:SeqIO\\_GenBank\\_Online\\]\n",
    "and [EFetch: Downloading full records from Entrez](#EFetch:-Downloading-full-records-from-Entrez)). From the *Cypripedioideae* example above, we can\n",
    "download GenBank record 186972394 using `Bio.Entrez.efetch`:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LOCUS       EU490707                1302 bp    DNA     linear   PLN 15-JAN-2009\n",
      "DEFINITION  Selenipedium aequinoctiale maturase K (matK) gene, partial cds;\n",
      "            chloroplast.\n",
      "ACCESSION   EU490707\n",
      "VERSION     EU490707.1  GI:186972394\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Selenipedium aequinoctiale\n",
      "  ORGANISM  Selenipedium aequinoctiale\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;\n",
      "            Cypripedioideae; Selenipedium.\n",
      "REFERENCE   1  (bases 1 to 1302)\n",
      "  AUTHORS   Neubig,K.M., Whitten,W.M., Carlsward,B.S., Blanco,M.A., Endara,L.,\n",
      "            Williams,N.H. and Moore,M.\n",
      "  TITLE     Phylogenetic utility of ycf1 in orchids: a plastid gene more\n",
      "            variable than matK\n",
      "  JOURNAL   Plant Syst. Evol. 277 (1-2), 75-84 (2009)\n",
      "REFERENCE   2  (bases 1 to 1302)\n",
      "  AUTHORS   Neubig,K.M., Whitten,W.M., Carlsward,B.S., Blanco,M.A.,\n",
      "            Endara,C.L., Williams,N.H. and Moore,M.J.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (14-FEB-2008) Department of Botany, University of\n",
      "            Florida, 220 Bartram Hall, Gainesville, FL 32611-8526, USA\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1302\n",
      "                     /organism=\"Selenipedium aequinoctiale\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /specimen_voucher=\"FLAS:Blanco 2475\"\n",
      "                     /db_xref=\"taxon:256374\"\n",
      "     gene            <1..>1302\n",
      "                     /gene=\"matK\"\n",
      "     CDS             <1..>1302\n",
      "                     /gene=\"matK\"\n",
      "                     /codon_start=1\n",
      "                     /transl_table=11\n",
      "                     /product=\"maturase K\"\n",
      "                     /protein_id=\"ACC99456.1\"\n",
      "                     /db_xref=\"GI:186972395\"\n",
      "                     /translation=\"IFYEPVEIFGYDNKSSLVLVKRLITRMYQQNFLISSVNDSNQKG\n",
      "                     FWGHKHFFSSHFSSQMVSEGFGVILEIPFSSQLVSSLEEKKIPKYQNLRSIHSIFPFL\n",
      "                     EDKFLHLNYVSDLLIPHPIHLEILVQILQCRIKDVPSLHLLRLLFHEYHNLNSLITSK\n",
      "                     KFIYAFSKRKKRFLWLLYNSYVYECEYLFQFLRKQSSYLRSTSSGVFLERTHLYVKIE\n",
      "                     HLLVVCCNSFQRILCFLKDPFMHYVRYQGKAILASKGTLILMKKWKFHLVNFWQSYFH\n",
      "                     FWSQPYRIHIKQLSNYSFSFLGYFSSVLENHLVVRNQMLENSFIINLLTKKFDTIAPV\n",
      "                     ISLIGSLSKAQFCTVLGHPISKPIWTDFSDSDILDRFCRICRNLCRYHSGSSKKQVLY\n",
      "                     RIKYILRLSCARTLARKHKSTVRTFMRRLGSGLLEEFFMEEE\"\n",
      "ORIGIN      \n",
      "        1 attttttacg aacctgtgga aatttttggt tatgacaata aatctagttt agtacttgtg\n",
      "       61 aaacgtttaa ttactcgaat gtatcaacag aattttttga tttcttcggt taatgattct\n",
      "      121 aaccaaaaag gattttgggg gcacaagcat tttttttctt ctcatttttc ttctcaaatg\n",
      "      181 gtatcagaag gttttggagt cattctggaa attccattct cgtcgcaatt agtatcttct\n",
      "      241 cttgaagaaa aaaaaatacc aaaatatcag aatttacgat ctattcattc aatatttccc\n",
      "      301 tttttagaag acaaattttt acatttgaat tatgtgtcag atctactaat accccatccc\n",
      "      361 atccatctgg aaatcttggt tcaaatcctt caatgccgga tcaaggatgt tccttctttg\n",
      "      421 catttattgc gattgctttt ccacgaatat cataatttga atagtctcat tacttcaaag\n",
      "      481 aaattcattt acgccttttc aaaaagaaag aaaagattcc tttggttact atataattct\n",
      "      541 tatgtatatg aatgcgaata tctattccag tttcttcgta aacagtcttc ttatttacga\n",
      "      601 tcaacatctt ctggagtctt tcttgagcga acacatttat atgtaaaaat agaacatctt\n",
      "      661 ctagtagtgt gttgtaattc ttttcagagg atcctatgct ttctcaagga tcctttcatg\n",
      "      721 cattatgttc gatatcaagg aaaagcaatt ctggcttcaa agggaactct tattctgatg\n",
      "      781 aagaaatgga aatttcatct tgtgaatttt tggcaatctt attttcactt ttggtctcaa\n",
      "      841 ccgtatagga ttcatataaa gcaattatcc aactattcct tctcttttct ggggtatttt\n",
      "      901 tcaagtgtac tagaaaatca tttggtagta agaaatcaaa tgctagagaa ttcatttata\n",
      "      961 ataaatcttc tgactaagaa attcgatacc atagccccag ttatttctct tattggatca\n",
      "     1021 ttgtcgaaag ctcaattttg tactgtattg ggtcatccta ttagtaaacc gatctggacc\n",
      "     1081 gatttctcgg attctgatat tcttgatcga ttttgccgga tatgtagaaa tctttgtcgt\n",
      "     1141 tatcacagcg gatcctcaaa aaaacaggtt ttgtatcgta taaaatatat acttcgactt\n",
      "     1201 tcgtgtgcta gaactttggc acggaaacat aaaagtacag tacgcacttt tatgcgaaga\n",
      "     1261 ttaggttcgg gattattaga agaattcttt atggaagaag aa\n",
      "//\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.efetch(db=\"nucleotide\", id=\"186972394\", rettype=\"gb\", retmode=\"text\")\n",
    "print(handle.read())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The arguments `rettype=\"gb\"` and `retmode=\"text\"` let us download this\n",
    "record in the GenBank format.\n",
    "\n",
    "Note that until Easter 2009, the Entrez EFetch API let you use “genbank”\n",
    "as the return type, however the NCBI now insist on using the official\n",
    "return types of “gb” or “gbwithparts” (or “gp” for proteins) as\n",
    "described on online. Also not that until Feb 2012, the Entrez EFetch API\n",
    "would default to returning plain text files, but now defaults to XML.\n",
    "\n",
    "Alternatively, you could for example use `rettype=\"fasta\"` to get the\n",
    "Fasta-format; see the [EFetch Sequences Help\n",
    "page](http://www.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html)\n",
    "for other options. Remember – the available formats depend on which\n",
    "database you are downloading from - see the main [EFetch Help\n",
    "page](http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html).\n",
    "\n",
    "If you fetch the record in one of the formats accepted by `Bio.SeqIO`\n",
    "(see Chapter \\[chapter:Bio.SeqIO\\]), you could directly parse it into a\n",
    "`SeqRecord`:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ID: EU490707.1\n",
      "Name: EU490707\n",
      "Description: Selenipedium aequinoctiale maturase K (matK) gene, partial cds; chloroplast.\n",
      "Number of features: 3\n",
      "/gi=186972394\n",
      "/taxonomy=['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta', 'Tracheophyta', 'Spermatophyta', 'Magnoliophyta', 'Liliopsida', 'Asparagales', 'Orchidaceae', 'Cypripedioideae', 'Selenipedium']\n",
      "/date=15-JAN-2009\n",
      "/references=[Reference(title='Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK', ...), Reference(title='Direct Submission', ...)]\n",
      "/organism=Selenipedium aequinoctiale\n",
      "/sequence_version=1\n",
      "/accessions=['EU490707']\n",
      "/data_file_division=PLN\n",
      "/source=chloroplast Selenipedium aequinoctiale\n",
      "/keywords=['']\n",
      "Seq('ATTTTTTACGAACCTGTGGAAATTTTTGGTTATGACAATAAATCTAGTTTAGTA...GAA', IUPACAmbiguousDNA())\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez, SeqIO\n",
    "handle = Entrez.efetch(db=\"nucleotide\", id=\"186972394\", rettype=\"gb\", retmode=\"text\")\n",
    "record = SeqIO.read(handle, \"genbank\")\n",
    "handle.close()\n",
    "print(record)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Note that a more typical use would be to save the sequence data to a\n",
    "local file, and *then* parse it with `Bio.SeqIO`. This can save you\n",
    "having to re-download the same file repeatedly while working on your\n",
    "script, and places less load on the NCBI’s servers. For example:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "__exit__",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-23-d6d046a39755>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      6\u001b[0m \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0mos\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0misfile\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      7\u001b[0m     \u001b[1;31m# Downloading...\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 8\u001b[1;33m     \u001b[1;32mwith\u001b[0m \u001b[0mEntrez\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mefetch\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdb\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"nucleotide\"\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mid\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"186972394\"\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mrettype\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"gb\"\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mretmode\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\"text\"\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mnet_handle\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      9\u001b[0m         \u001b[1;32mwith\u001b[0m \u001b[0mopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m\"w\"\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mas\u001b[0m \u001b[0mout_handle\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     10\u001b[0m             \u001b[0mout_handle\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mnet_handle\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mAttributeError\u001b[0m: __exit__"
     ]
    }
   ],
   "source": [
    "import os\n",
    "from Bio import SeqIO\n",
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "filename = \"gi_186972394.gbk\"\n",
    "if not os.path.isfile(filename):\n",
    "    # Downloading...\n",
    "    with Entrez.efetch(db=\"nucleotide\",id=\"186972394\",rettype=\"gb\", retmode=\"text\") as net_handle:\n",
    "        with open(filename, \"w\") as out_handle:\n",
    "            out_handle.write(net_handle.read())\n",
    "        print(\"Saved\")\n",
    "\n",
    "print(\"Parsing...\")\n",
    "record = SeqIO.read(filename, \"genbank\")\n",
    "print(record)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "To get the output in XML format, which you can parse using the\n",
    "`Bio.Entrez.read()` function, use `retmode=\"xml\"`:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Selenipedium aequinoctiale maturase K (matK) gene, partial cds; chloroplast'"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "handle = Entrez.efetch(db=\"nucleotide\", id=\"186972394\", retmode=\"xml\")\n",
    "record = Entrez.read(handle)\n",
    "handle.close()\n",
    "record[0][\"GBSeq_definition\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'chloroplast Selenipedium aequinoctiale'"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[0][\"GBSeq_source\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "So, that dealt with sequences. For examples of parsing file formats\n",
    "specific to the other databases (e.g. the `MEDLINE` format used in\n",
    "PubMed), see Section [Specialized parsers](#Specialized-parsers).\n",
    "\n",
    "If you want to perform a search with `Bio.Entrez.esearch()`, and then\n",
    "download the records with `Bio.Entrez.efetch()`, you should use the\n",
    "WebEnv history feature – see Section [History and WebEnv](#Using-the-history-and-WebEnv).\n",
    "\n",
    "## ELink: Searching for related items in NCBI Entrez\n",
    "\n",
    "ELink, available from Biopython as `Bio.Entrez.elink()`, can be used to\n",
    "find related items in the NCBI Entrez databases. For example, you can us\n",
    "this to find nucleotide entries for an entry in the gene database, and\n",
    "other cool stuff.\n",
    "\n",
    "Let’s use ELink to find articles related to the Biopython application\n",
    "note published in *Bioinformatics* in 2009. The PubMed ID of this\n",
    "article is 19304878:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dict_keys(['ERROR', 'LinkSetDbHistory', 'IdList', 'LinkSetDb', 'DbFrom'])\n",
      "The record is from the pubmed database.\n",
      "The IdList is ['19304878'].\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"\n",
    "pmid = \"19304878\"\n",
    "record = Entrez.read(Entrez.elink(dbfrom=\"pubmed\", id=pmid))\n",
    "print(record[0].keys())\n",
    "print('The record is from the {} database.'.format(record[0][\"DbFrom\"]))\n",
    "print('The IdList is {}.'.format(record[0][\"IdList\"]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The `record` variable consists of a Python list, one for each database\n",
    "in which we searched. Since we specified only one PubMed ID to search\n",
    "for, `record` contains only one item. This item is a dictionary\n",
    "containing information about our search term, as well as all the related\n",
    "items that were found:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The `\"LinkSetDb\"` key contains the search results, stored as a list\n",
    "consisting of one item for each target database. In our search results,\n",
    "we only find hits in the PubMed database (although sub-divided into\n",
    "categories):\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "There are 8 search results\n",
      "pubmed pubmed_pubmed 224\n",
      "pubmed pubmed_pubmed_alsoviewed 3\n",
      "pubmed pubmed_pubmed_citedin 276\n",
      "pubmed pubmed_pubmed_combined 6\n",
      "pubmed pubmed_pubmed_five 6\n",
      "pubmed pubmed_pubmed_refs 17\n",
      "pubmed pubmed_pubmed_reviews 8\n",
      "pubmed pubmed_pubmed_reviews_five 6\n"
     ]
    }
   ],
   "source": [
    "print('There are {} search results'.format(len(record[0][\"LinkSetDb\"])))\n",
    "for linksetdb in record[0][\"LinkSetDb\"]:\n",
    "    print(linksetdb[\"DbTo\"], linksetdb[\"LinkName\"], len(linksetdb[\"Link\"]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The actual search results are stored as under the `\"Link\"` key. In\n",
    "total, 110 items were found under standard search. Let’s now at the\n",
    "first search result:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'Id': '19304878'}"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[0][\"LinkSetDb\"][0][\"Link\"][0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "This is the article we searched for, which doesn’t help us much, so\n",
    "let’s look at the second search result:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'Id': '14630660'}"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[0][\"LinkSetDb\"][0][\"Link\"][1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "This paper, with PubMed ID 14630660, is about the Biopython PDB parser.\n",
    "\n",
    "We can use a loop to print out all PubMed IDs:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "19304878\n",
      "14630660\n",
      "22909249\n",
      "20739307\n",
      "23023984\n",
      "18689808\n",
      "20733063\n",
      "19628504\n",
      "18251993\n",
      "15572471\n",
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      "25273102\n",
      "12368254\n",
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      "25110777\n",
      "21253560\n",
      "25132841\n",
      "25926788\n"
     ]
    }
   ],
   "source": [
    "for link in record[0][\"LinkSetDb\"][0][\"Link\"]:\n",
    "    print(link[\"Id\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Now that was nice, but personally I am often more interested to find out\n",
    "if a paper has been cited. Well, ELink can do that too – at least for\n",
    "journals in Pubmed Central (see Section \\[sec:elink-citations\\]).\n",
    "\n",
    "For help on ELink, see the [ELink help\n",
    "page](http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html).\n",
    "There is an entire sub-page just for the [link\n",
    "names](http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/entrezlinks.html),\n",
    "describing how different databases can be cross referenced.\n",
    "\n",
    "EGQuery: Global Query - counts for search terms\n",
    "-----------------------------------------------\n",
    "\n",
    "EGQuery provides counts for a search term in each of the Entrez\n",
    "databases (i.e. a global query). This is particularly useful to find out\n",
    "how many items your search terms would find in each database without\n",
    "actually performing lots of separate searches with ESearch (see the\n",
    "example in \\[subsec:entrez\\_example\\_genbank\\] below).\n",
    "\n",
    "In this example, we use `Bio.Entrez.egquery()` to obtain the counts for\n",
    "“Biopython”:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pubmed 21\n",
      "pmc 560\n",
      "mesh 0\n",
      "books 2\n",
      "pubmedhealth 2\n",
      "omim 0\n",
      "ncbisearch 0\n",
      "nuccore 0\n",
      "nucgss 0\n",
      "nucest 0\n",
      "protein 0\n",
      "genome 0\n",
      "structure 0\n",
      "taxonomy 0\n",
      "snp 0\n",
      "dbvar 0\n",
      "epigenomics 0\n",
      "gene 0\n",
      "sra 0\n",
      "biosystems 0\n",
      "unigene 0\n",
      "cdd 0\n",
      "clone 0\n",
      "popset 0\n",
      "geoprofiles 0\n",
      "gds 16\n",
      "homologene 0\n",
      "pccompound 0\n",
      "pcsubstance 0\n",
      "pcassay 0\n",
      "nlmcatalog 0\n",
      "probe 0\n",
      "gap 0\n",
      "proteinclusters 0\n",
      "bioproject 0\n",
      "biosample 0\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.egquery(term=\"biopython\")\n",
    "record = Entrez.read(handle)\n",
    "for row in record[\"eGQueryResult\"]:\n",
    "    print(row[\"DbName\"], row[\"Count\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "See the [EGQuery help\n",
    "page](http://www.ncbi.nlm.nih.gov/entrez/query/static/egquery_help.html)\n",
    "for more information.\n",
    "\n",
    "ESpell: Obtaining spelling suggestions\n",
    "--------------------------------------\n",
    "\n",
    "ESpell retrieves spelling suggestions. In this example, we use\n",
    "`Bio.Entrez.espell()` to obtain the correct spelling of Biopython:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'biopythooon'"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.espell(term=\"biopythooon\")\n",
    "record = Entrez.read(handle)\n",
    "record[\"Query\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'biopython'"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"CorrectedQuery\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "See the [ESpell help\n",
    "page](http://www.ncbi.nlm.nih.gov/entrez/query/static/espell_help.html)\n",
    "for more information. The main use of this is for GUI tools to provide\n",
    "automatic suggestions for search terms.\n",
    "\n",
    "Parsing huge Entrez XML files\n",
    "-----------------------------\n",
    "\n",
    "The `Entrez.read` function reads the entire XML file returned by Entrez\n",
    "into a single Python object, which is kept in memory. To parse Entrez\n",
    "XML files too large to fit in memory, you can use the function\n",
    "`Entrez.parse`. This is a generator function that reads records in the\n",
    "XML file one by one. This function is only useful if the XML file\n",
    "reflects a Python list object (in other words, if `Entrez.read` on a\n",
    "computer with infinite memory resources would return a Python list).\n",
    "\n",
    "For example, you can download the entire Entrez Gene database for a\n",
    "given organism as a file from NCBI’s ftp site. These files can be very\n",
    "large. As an example, on September 4, 2009, the file\n",
    "`Homo_sapiens.ags.gz`, containing the Entrez Gene database for human,\n",
    "had a size of 116576 kB. This file, which is in the `ASN` format, can be\n",
    "converted into an XML file using NCBI’s `gene2xml` program (see NCBI’s\n",
    "ftp site for more information):\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "gene2xml -b T -i Homo_sapiens.ags -o Homo_sapiens.xml\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The resulting XML file has a size of 6.1 GB. Attempting `Entrez.read` on\n",
    "this file will result in a `MemoryError` on many computers.\n",
    "\n",
    "The XML file `Homo_sapiens.xml` consists of a list of Entrez gene\n",
    "records, each corresponding to one Entrez gene in human. `Entrez.parse`\n",
    "retrieves these gene records one by one. You can then print out or store\n",
    "the relevant information in each record by iterating over the records.\n",
    "For example, this script iterates over the Entrez gene records and\n",
    "prints out the gene numbers and names for all current genes:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<font color='red'>TODO: need alternate example, download option or ...</font>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "```python\n",
    "from Bio import Entrez\n",
    "handle = open(\"Homo_sapiens.xml\")\n",
    "records = Entrez.parse(handle)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "```python\n",
    "for record in records:\n",
    "    status = record['Entrezgene_track-info']['Gene-track']['Gene-track_status']\n",
    "    if status.attributes['value']=='discontinued':\n",
    "        continue\n",
    "    geneid = record['Entrezgene_track-info']['Gene-track']['Gene-track_geneid']\n",
    "    genename = record['Entrezgene_gene']['Gene-ref']['Gene-ref_locus']\n",
    "    print(geneid, genename)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "This will print:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "1 A1BG\n",
    "2 A2M\n",
    "3 A2MP\n",
    "8 AA\n",
    "9 NAT1\n",
    "10 NAT2\n",
    "11 AACP\n",
    "12 SERPINA3\n",
    "13 AADAC\n",
    "14 AAMP\n",
    "15 AANAT\n",
    "16 AARS\n",
    "17 AAVS1\n",
    "...\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Handling errors\n",
    "---------------\n",
    "\n",
    "Three things can go wrong when parsing an XML file:\n",
    "\n",
    "-   The file may not be an XML file to begin with;\n",
    "\n",
    "-   The file may end prematurely or otherwise be corrupted;\n",
    "\n",
    "-   The file may be correct XML, but contain items that are not\n",
    "    represented in the associated DTD.\n",
    "\n",
    "The first case occurs if, for example, you try to parse a Fasta file as\n",
    "if it were an XML file:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "We are expecting to get NotXMLError\n",
      "Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in XML format.\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "from Bio.Entrez.Parser import NotXMLError\n",
    "handle = open(\"data/NC_005816.fna\", 'rb') # a Fasta file\n",
    "try:\n",
    "    record = Entrez.read(handle)\n",
    "except NotXMLError as e:\n",
    "    print('We are expecting to get NotXMLError')\n",
    "    print(e)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Here, the parser didn’t find the `<?xml ...` tag with which an XML file\n",
    "is supposed to start, and therefore decides (correctly) that the file is\n",
    "not an XML file.\n",
    "\n",
    "When your file is in the XML format but is corrupted (for example, by\n",
    "ending prematurely), the parser will raise a CorruptedXMLError. Here is\n",
    "an example of an XML file that ends prematurely:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```xml\n",
    "<?xml version=\"1.0\"?>\n",
    "<!DOCTYPE eInfoResult PUBLIC \"-//NLM//DTD eInfoResult, 11 May 2002//EN\" \"http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd\">\n",
    "<eInfoResult>\n",
    "<DbList>\n",
    "        <DbName>pubmed</DbName>\n",
    "        <DbName>protein</DbName>\n",
    "        <DbName>nucleotide</DbName>\n",
    "        <DbName>nuccore</DbName>\n",
    "        <DbName>nucgss</DbName>\n",
    "        <DbName>nucest</DbName>\n",
    "        <DbName>structure</DbName>\n",
    "        <DbName>genome</DbName>\n",
    "        <DbName>books</DbName>\n",
    "        <DbName>cancerchromosomes</DbName>\n",
    "        <DbName>cdd</DbName>\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "which will generate the following traceback:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "```python\n",
    "---------------------------------------------------------------------------\n",
    "ExpatError                                Traceback (most recent call last)\n",
    "/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/Entrez/Parser.py in read(self, handle)\n",
    "    214         try:\n",
    "--> 215             self.parser.ParseFile(handle)\n",
    "    216         except expat.ExpatError as e:\n",
    "\n",
    "ExpatError: syntax error: line 1, column 0\n",
    "\n",
    "During handling of the above exception, another exception occurred:\n",
    "\n",
    "NotXMLError                               Traceback (most recent call last)\n",
    "<ipython-input-63-ac0523d72453> in <module>()\n",
    "----> 1 Entrez.read(handle)\n",
    "\n",
    "/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/Entrez/__init__.py in read(handle, validate)\n",
    "    419     from .Parser import DataHandler\n",
    "    420     handler = DataHandler(validate)\n",
    "--> 421     record = handler.read(handle)\n",
    "    422     return record\n",
    "    423 \n",
    "\n",
    "/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/Entrez/Parser.py in read(self, handle)\n",
    "    223                 # We have not seen the initial <!xml declaration, so probably\n",
    "    224                 # the input data is not in XML format.\n",
    "--> 225                 raise NotXMLError(e)\n",
    "    226         try:\n",
    "    227             return self.object\n",
    "\n",
    "NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in XML format.\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Note that the error message tells you at what point in the XML file the\n",
    "error was detected.\n",
    "\n",
    "The third type of error occurs if the XML file contains tags that do not\n",
    "have a description in the corresponding DTD file. This is an example of\n",
    "such an XML file:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```xml\n",
    "<?xml version=\"1.0\"?>\n",
    "<!DOCTYPE eInfoResult PUBLIC \"-//NLM//DTD eInfoResult, 11 May 2002//EN\" \"http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd\">\n",
    "<eInfoResult>\n",
    "        <DbInfo>\n",
    "        <DbName>pubmed</DbName>\n",
    "        <MenuName>PubMed</MenuName>\n",
    "        <Description>PubMed bibliographic record</Description>\n",
    "        <Count>20161961</Count>\n",
    "        <LastUpdate>2010/09/10 04:52</LastUpdate>\n",
    "        <FieldList>\n",
    "                <Field>\n",
    "...\n",
    "                </Field>\n",
    "        </FieldList>\n",
    "        <DocsumList>\n",
    "                <Docsum>\n",
    "                        <DsName>PubDate</DsName>\n",
    "                        <DsType>4</DsType>\n",
    "                        <DsTypeName>string</DsTypeName>\n",
    "                </Docsum>\n",
    "                <Docsum>\n",
    "                        <DsName>EPubDate</DsName>\n",
    "...\n",
    "        </DbInfo>\n",
    "</eInfoResult>\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "In this file, for some reason the tag `<DocsumList>` (and several\n",
    "others) are not listed in the DTD file `eInfo_020511.dtd`, which is\n",
    "specified on the second line as the DTD for this XML file. By default,\n",
    "the parser will stop and raise a ValidationError if it cannot find some\n",
    "tag in the DTD:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "```python\n",
    "from Bio import Entrez\n",
    "handle = open(\"data/einfo3.xml\", 'rb')\n",
    "record = Entrez.read(handle)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```python\n",
    "---------------------------------------------------------------------------\n",
    "ValidationError                           Traceback (most recent call last)\n",
    "<ipython-input-65-cfb96ec3d2ca> in <module>()\n",
    "      1 from Bio import Entrez\n",
    "      2 handle = open(\"data/einfo3.xml\", 'rb')\n",
    "----> 3 record = Entrez.read(handle)\n",
    "\n",
    "/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/Entrez/__init__.py in read(handle, validate)\n",
    "    419     from .Parser import DataHandler\n",
    "    420     handler = DataHandler(validate)\n",
    "--> 421     record = handler.read(handle)\n",
    "    422     return record\n",
    "    423 \n",
    "\n",
    "/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/Entrez/Parser.py in read(self, handle)\n",
    "    213             raise IOError(\"Can't parse a closed handle\")\n",
    "    214         try:\n",
    "--> 215             self.parser.ParseFile(handle)\n",
    "    216         except expat.ExpatError as e:\n",
    "    217             if self.parser.StartElementHandler:\n",
    "\n",
    "-------src-dir--------/Python-3.5.1/Modules/pyexpat.c in StartElement()\n",
    "\n",
    "/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/Entrez/Parser.py in startElementHandler(self, name, attrs)\n",
    "    348             # Element not found in DTD\n",
    "    349             if self.validating:\n",
    "--> 350                 raise ValidationError(name)\n",
    "    351             else:\n",
    "    352                 # this will not be stored in the record\n",
    "\n",
    "ValidationError: Failed to find tag 'DocsumList' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Optionally, you can instruct the parser to skip such tags instead of\n",
    "raising a ValidationError. This is done by calling `Entrez.read` or\n",
    "`Entrez.parse` with the argument `validate` equal to False:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from Bio import Entrez\n",
    "handle = open(\"data/einfo3.xml\", 'rb')\n",
    "record = Entrez.read(handle, validate=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Of course, the information contained in the XML tags that are not in the\n",
    "DTD are not present in the record returned by `Entrez.read`.\n",
    "\n",
    "Specialized parsers\n",
    "------------------\n",
    "\n",
    "The `Bio.Entrez.read()` function can parse most (if not all) XML output\n",
    "returned by Entrez. Entrez typically allows you to retrieve records in\n",
    "other formats, which may have some advantages compared to the XML format\n",
    "in terms of readability (or download size).\n",
    "\n",
    "To request a specific file format from Entrez using\n",
    "`Bio.Entrez.efetch()` requires specifying the `rettype` and/or `retmode`\n",
    "optional arguments. The different combinations are described for each\n",
    "database type on the [NCBI efetch\n",
    "webpage](http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html).\n",
    "\n",
    "One obvious case is you may prefer to download sequences in the FASTA or\n",
    "GenBank/GenPept plain text formats (which can then be parsed with\n",
    "`Bio.SeqIO`, see Sections \\[sec:SeqIO\\_GenBank\\_Online\\]\n",
    "and [EFetch: Downloading full records from Entrez](#EFetch:-Downloading-full-records-from-Entrez)). For the literature databases, Biopython contains a\n",
    "parser for the `MEDLINE` format used in PubMed.\n",
    "\n",
    "### Parsing Medline records {#subsec:entrez-and-medline}\n",
    "\n",
    "You can find the Medline parser in `Bio.Medline`. Suppose we want to\n",
    "parse the file `pubmed_result1.txt`, containing one Medline record. You\n",
    "can find this file in Biopython’s `Tests\\Medline` directory. The file\n",
    "looks like this:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "PMID- 12230038\n",
    "OWN - NLM\n",
    "STAT- MEDLINE\n",
    "DA  - 20020916\n",
    "DCOM- 20030606\n",
    "LR  - 20041117\n",
    "PUBM- Print\n",
    "IS  - 1467-5463 (Print)\n",
    "VI  - 3\n",
    "IP  - 3\n",
    "DP  - 2002 Sep\n",
    "TI  - The Bio* toolkits--a brief overview.\n",
    "PG  - 296-302\n",
    "AB  - Bioinformatics research is often difficult to do with commercial software. The\n",
    "      Open Source BioPerl, BioPython and Biojava projects provide toolkits with\n",
    "...\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "We first open the file and then parse it:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from Bio import Medline\n",
    "with open(\"data/pubmed_result1.txt\") as handle:\n",
    "    record = Medline.read(handle)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The `record` now contains the Medline record as a Python dictionary:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'12230038'"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"PMID\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.'"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"AB\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The key names used in a Medline record can be rather obscure; use\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on Record in module Bio.Medline object:\n",
      "\n",
      "class Record(builtins.dict)\n",
      " |  A dictionary holding information from a Medline record.\n",
      " |  \n",
      " |  All data are stored under the mnemonic appearing in the Medline\n",
      " |  file. These mnemonics have the following interpretations:\n",
      " |  \n",
      " |  ========= ==============================\n",
      " |  Mnemonic  Description\n",
      " |  --------- ------------------------------\n",
      " |  AB        Abstract\n",
      " |  CI        Copyright Information\n",
      " |  AD        Affiliation\n",
      " |  IRAD      Investigator Affiliation\n",
      " |  AID       Article Identifier\n",
      " |  AU        Author\n",
      " |  FAU       Full Author\n",
      " |  CN        Corporate Author\n",
      " |  DCOM      Date Completed\n",
      " |  DA        Date Created\n",
      " |  LR        Date Last Revised\n",
      " |  DEP       Date of Electronic Publication\n",
      " |  DP        Date of Publication\n",
      " |  EDAT      Entrez Date\n",
      " |  GS        Gene Symbol\n",
      " |  GN        General Note\n",
      " |  GR        Grant Number\n",
      " |  IR        Investigator Name\n",
      " |  FIR       Full Investigator Name\n",
      " |  IS        ISSN\n",
      " |  IP        Issue\n",
      " |  TA        Journal Title Abbreviation\n",
      " |  JT        Journal Title\n",
      " |  LA        Language\n",
      " |  LID       Location Identifier\n",
      " |  MID       Manuscript Identifier\n",
      " |  MHDA      MeSH Date\n",
      " |  MH        MeSH Terms\n",
      " |  JID       NLM Unique ID\n",
      " |  RF        Number of References\n",
      " |  OAB       Other Abstract\n",
      " |  OCI       Other Copyright Information\n",
      " |  OID       Other ID\n",
      " |  OT        Other Term\n",
      " |  OTO       Other Term Owner\n",
      " |  OWN       Owner\n",
      " |  PG        Pagination\n",
      " |  PS        Personal Name as Subject\n",
      " |  FPS       Full Personal Name as Subject\n",
      " |  PL        Place of Publication\n",
      " |  PHST      Publication History Status\n",
      " |  PST       Publication Status\n",
      " |  PT        Publication Type\n",
      " |  PUBM      Publishing Model\n",
      " |  PMC       PubMed Central Identifier\n",
      " |  PMID      PubMed Unique Identifier\n",
      " |  RN        Registry Number/EC Number\n",
      " |  NM        Substance Name\n",
      " |  SI        Secondary Source ID\n",
      " |  SO        Source\n",
      " |  SFM       Space Flight Mission\n",
      " |  STAT      Status\n",
      " |  SB        Subset\n",
      " |  TI        Title\n",
      " |  TT        Transliterated Title\n",
      " |  VI        Volume\n",
      " |  CON       Comment on\n",
      " |  CIN       Comment in\n",
      " |  EIN       Erratum in\n",
      " |  EFR       Erratum for\n",
      " |  CRI       Corrected and Republished in\n",
      " |  CRF       Corrected and Republished from\n",
      " |  PRIN      Partial retraction in\n",
      " |  PROF      Partial retraction of\n",
      " |  RPI       Republished in\n",
      " |  RPF       Republished from\n",
      " |  RIN       Retraction in\n",
      " |  ROF       Retraction of\n",
      " |  UIN       Update in\n",
      " |  UOF       Update of\n",
      " |  SPIN      Summary for patients in\n",
      " |  ORI       Original report in\n",
      " |  ========= ==============================\n",
      " |  \n",
      " |  Method resolution order:\n",
      " |      Record\n",
      " |      builtins.dict\n",
      " |      builtins.object\n",
      " |  \n",
      " |  Data descriptors defined here:\n",
      " |  \n",
      " |  __dict__\n",
      " |      dictionary for instance variables (if defined)\n",
      " |  \n",
      " |  __weakref__\n",
      " |      list of weak references to the object (if defined)\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Methods inherited from builtins.dict:\n",
      " |  \n",
      " |  __contains__(self, key, /)\n",
      " |      True if D has a key k, else False.\n",
      " |  \n",
      " |  __delitem__(self, key, /)\n",
      " |      Delete self[key].\n",
      " |  \n",
      " |  __eq__(self, value, /)\n",
      " |      Return self==value.\n",
      " |  \n",
      " |  __ge__(self, value, /)\n",
      " |      Return self>=value.\n",
      " |  \n",
      " |  __getattribute__(self, name, /)\n",
      " |      Return getattr(self, name).\n",
      " |  \n",
      " |  __getitem__(...)\n",
      " |      x.__getitem__(y) <==> x[y]\n",
      " |  \n",
      " |  __gt__(self, value, /)\n",
      " |      Return self>value.\n",
      " |  \n",
      " |  __init__(self, /, *args, **kwargs)\n",
      " |      Initialize self.  See help(type(self)) for accurate signature.\n",
      " |  \n",
      " |  __iter__(self, /)\n",
      " |      Implement iter(self).\n",
      " |  \n",
      " |  __le__(self, value, /)\n",
      " |      Return self<=value.\n",
      " |  \n",
      " |  __len__(self, /)\n",
      " |      Return len(self).\n",
      " |  \n",
      " |  __lt__(self, value, /)\n",
      " |      Return self<value.\n",
      " |  \n",
      " |  __ne__(self, value, /)\n",
      " |      Return self!=value.\n",
      " |  \n",
      " |  __new__(*args, **kwargs) from builtins.type\n",
      " |      Create and return a new object.  See help(type) for accurate signature.\n",
      " |  \n",
      " |  __repr__(self, /)\n",
      " |      Return repr(self).\n",
      " |  \n",
      " |  __setitem__(self, key, value, /)\n",
      " |      Set self[key] to value.\n",
      " |  \n",
      " |  __sizeof__(...)\n",
      " |      D.__sizeof__() -> size of D in memory, in bytes\n",
      " |  \n",
      " |  clear(...)\n",
      " |      D.clear() -> None.  Remove all items from D.\n",
      " |  \n",
      " |  copy(...)\n",
      " |      D.copy() -> a shallow copy of D\n",
      " |  \n",
      " |  fromkeys(iterable, value=None, /) from builtins.type\n",
      " |      Returns a new dict with keys from iterable and values equal to value.\n",
      " |  \n",
      " |  get(...)\n",
      " |      D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None.\n",
      " |  \n",
      " |  items(...)\n",
      " |      D.items() -> a set-like object providing a view on D's items\n",
      " |  \n",
      " |  keys(...)\n",
      " |      D.keys() -> a set-like object providing a view on D's keys\n",
      " |  \n",
      " |  pop(...)\n",
      " |      D.pop(k[,d]) -> v, remove specified key and return the corresponding value.\n",
      " |      If key is not found, d is returned if given, otherwise KeyError is raised\n",
      " |  \n",
      " |  popitem(...)\n",
      " |      D.popitem() -> (k, v), remove and return some (key, value) pair as a\n",
      " |      2-tuple; but raise KeyError if D is empty.\n",
      " |  \n",
      " |  setdefault(...)\n",
      " |      D.setdefault(k[,d]) -> D.get(k,d), also set D[k]=d if k not in D\n",
      " |  \n",
      " |  update(...)\n",
      " |      D.update([E, ]**F) -> None.  Update D from dict/iterable E and F.\n",
      " |      If E is present and has a .keys() method, then does:  for k in E: D[k] = E[k]\n",
      " |      If E is present and lacks a .keys() method, then does:  for k, v in E: D[k] = v\n",
      " |      In either case, this is followed by: for k in F:  D[k] = F[k]\n",
      " |  \n",
      " |  values(...)\n",
      " |      D.values() -> an object providing a view on D's values\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data and other attributes inherited from builtins.dict:\n",
      " |  \n",
      " |  __hash__ = None\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(record)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "for a brief summary.\n",
    "\n",
    "To parse a file containing multiple Medline records, you can use the\n",
    "`parse` function instead:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "A high level interface to SCOP and ASTRAL implemented in python.\n",
      "GenomeDiagram: a python package for the visualization of large-scale genomic data.\n",
      "Open source clustering software.\n",
      "PDB file parser and structure class implemented in Python.\n"
     ]
    }
   ],
   "source": [
    "from Bio import Medline\n",
    "with open(\"data/pubmed_result2.txt\") as handle:\n",
    "    for record in Medline.parse(handle):\n",
    "        print(record[\"TI\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Instead of parsing Medline records stored in files, you can also parse\n",
    "Medline records downloaded by `Bio.Entrez.efetch`. For example, let’s\n",
    "look at all Medline records in PubMed related to Biopython:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['24929426', '24497503', '24267035', '24194598', '23842806', '23157543', '22909249', '22399473', '21666252', '21210977', '20015970', '19811691', '19773334', '19304878', '18606172', '21585724', '16403221', '16377612', '14871861', '14630660']"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.esearch(db=\"pubmed\", term=\"biopython\")\n",
    "record = Entrez.read(handle)\n",
    "record[\"IdList\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "We now use `Bio.Entrez.efetch` to download these Medline records:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "idlist = record[\"IdList\"]\n",
    "handle = Entrez.efetch(db=\"pubmed\", id=idlist, rettype=\"medline\", retmode=\"text\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Here, we specify `rettype=\"medline\", retmode=\"text\"` to obtain the\n",
    "Medline records in plain-text Medline format. Now we use `Bio.Medline`\n",
    "to parse these records:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['Waldmann J', 'Gerken J', 'Hankeln W', 'Schweer T', 'Glockner FO']\n",
      "['Mielke CJ', 'Mandarino LJ', 'Dinu V']\n",
      "['Gajda MJ']\n",
      "['Mathelier A', 'Zhao X', 'Zhang AW', 'Parcy F', 'Worsley-Hunt R', 'Arenillas DJ', 'Buchman S', 'Chen CY', 'Chou A', 'Ienasescu H', 'Lim J', 'Shyr C', 'Tan G', 'Zhou M', 'Lenhard B', 'Sandelin A', 'Wasserman WW']\n",
      "['Morales HF', 'Giovambattista G']\n",
      "['Baldwin S', 'Revanna R', 'Thomson S', 'Pither-Joyce M', 'Wright K', 'Crowhurst R', 'Fiers M', 'Chen L', 'Macknight R', 'McCallum JA']\n",
      "['Talevich E', 'Invergo BM', 'Cock PJ', 'Chapman BA']\n",
      "['Prins P', 'Goto N', 'Yates A', 'Gautier L', 'Willis S', 'Fields C', 'Katayama T']\n",
      "['Schmitt T', 'Messina DN', 'Schreiber F', 'Sonnhammer EL']\n",
      "['Antao T']\n",
      "['Cock PJ', 'Fields CJ', 'Goto N', 'Heuer ML', 'Rice PM']\n",
      "['Jankun-Kelly TJ', 'Lindeman AD', 'Bridges SM']\n",
      "['Korhonen J', 'Martinmaki P', 'Pizzi C', 'Rastas P', 'Ukkonen E']\n",
      "['Cock PJ', 'Antao T', 'Chang JT', 'Chapman BA', 'Cox CJ', 'Dalke A', 'Friedberg I', 'Hamelryck T', 'Kauff F', 'Wilczynski B', 'de Hoon MJ']\n",
      "['Munteanu CR', 'Gonzalez-Diaz H', 'Magalhaes AL']\n",
      "['Faircloth BC']\n",
      "['Casbon JA', 'Crooks GE', 'Saqi MA']\n",
      "['Pritchard L', 'White JA', 'Birch PR', 'Toth IK']\n",
      "['de Hoon MJ', 'Imoto S', 'Nolan J', 'Miyano S']\n",
      "['Hamelryck T', 'Manderick B']\n"
     ]
    }
   ],
   "source": [
    "from Bio import Medline\n",
    "records = Medline.parse(handle)\n",
    "for record in records:\n",
    "    print(record[\"AU\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "For comparison, here we show an example using the XML format:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.\n",
      "AMASS: a database for investigating protein structures.\n",
      "HPDB-Haskell library for processing atomic biomolecular structures in Protein Data Bank format.\n",
      "JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.\n",
      "BioSmalltalk: a pure object system and library for bioinformatics.\n",
      "A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.).\n",
      "Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.\n",
      "Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.\n",
      "Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information.\n",
      "interPopula: a Python API to access the HapMap Project dataset.\n",
      "The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.\n",
      "Exploratory visual analysis of conserved domains on multiple sequence alignments.\n",
      "MOODS: fast search for position weight matrix matches in DNA sequences.\n",
      "Biopython: freely available Python tools for computational molecular biology and bioinformatics.\n",
      "Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices.\n",
      "msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.\n",
      "A high level interface to SCOP and ASTRAL implemented in python.\n",
      "GenomeDiagram: a python package for the visualization of large-scale genomic data.\n",
      "Open source clustering software.\n",
      "PDB file parser and structure class implemented in Python.\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.esearch(db=\"pubmed\", term=\"biopython\")\n",
    "record = Entrez.read(handle)\n",
    "idlist = record[\"IdList\"]\n",
    "handle = Entrez.efetch(db=\"pubmed\", id=idlist, rettype=\"medline\", retmode=\"xml\")\n",
    "records = Entrez.read(handle)\n",
    "for record in records:\n",
    "    print(record[\"MedlineCitation\"][\"Article\"][\"ArticleTitle\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Note that in both of these examples, for simplicity we have naively\n",
    "combined ESearch and EFetch. In this situation, the NCBI would expect\n",
    "you to use their history feature, as illustrated in\n",
    "Section [History and WebEnv](#Using-the-history-and-WebEnv).\n",
    "\n",
    "### Parsing GEO records\n",
    "\n",
    "GEO ([Gene Expression Omnibus](http://www.ncbi.nlm.nih.gov/geo/)) is a\n",
    "data repository of high-throughput gene expression and hybridization\n",
    "array data. The `Bio.Geo` module can be used to parse GEO-formatted\n",
    "data.\n",
    "\n",
    "The following code fragment shows how to parse the example GEO file\n",
    "`GSE16.txt` into a record and print the record:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GEO Type: SAMPLE\n",
      "GEO Id: GSM804\n",
      "Sample_author: Antoine,M,Snijders\n",
      "\n",
      "Sample_author: Norma,,Nowak\n",
      "\n",
      "Sample_author: Richard,,Segraves\n",
      "\n",
      "Sample_author: Stephanie,,Blackwood\n",
      "\n",
      "Sample_author: Nils,,Brown\n",
      "\n",
      "Sample_author: Jeffery,,Conroy\n",
      "\n",
      "Sample_author: Greg,,Hamilton\n",
      "\n",
      "Sample_author: Anna,K,Hindle\n",
      "\n",
      "Sample_author: Bing,,Huey\n",
      "\n",
      "Sample_author: Karen,,Kimura\n",
      "\n",
      "Sample_author: Sindy,,Law\n",
      "\n",
      "Sample_author: Ken,,Myambo\n",
      "\n",
      "Sample_author: Joel,,Palmer\n",
      "\n",
      "Sample_author: Bauke,,Ylstra\n",
      "\n",
      "Sample_author: Jingzhu,P,Yue\n",
      "\n",
      "Sample_author: Joe,W,Gray\n",
      "\n",
      "Sample_author: Ajay,N,Jain\n",
      "\n",
      "Sample_author: Daniel,,Pinkel\n",
      "\n",
      "Sample_author: Donna,G,Albertson\n",
      "\n",
      "Sample_description: Coriell Cell Repositories cell line <a h\n",
      "ref=\"http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM05296\">GM05296</a>.\n",
      "\n",
      "Sample_description: Fibroblast cell line derived from a 1 mo\n",
      "nth old female with multiple congenital malformations, dysmorphic features, intr\n",
      "auterine growth retardation, heart murmur, cleft palate, equinovarus deformity, \n",
      "microcephaly, coloboma of right iris, clinodactyly, reduced RBC catalase activit\n",
      "y, and 1 copy of catalase gene.\n",
      "\n",
      "Sample_description: Chromosome abnormalities are present.\n",
      "\n",
      "Sample_description: Karyotype is 46,XX,-11,+der(11)inv ins(1\n",
      "1;10)(11pter> 11p13::10q21>10q24::11p13>11qter)mat\n",
      "\n",
      "Sample_organism: Homo sapiens\n",
      "\n",
      "Sample_platform_id: GPL28\n",
      "\n",
      "Sample_pubmed_id: 11687795\n",
      "\n",
      "Sample_series_id: GSE16\n",
      "\n",
      "Sample_status: Public on Feb 12 2002\n",
      "\n",
      "Sample_submission_date: Jan 17 2002\n",
      "\n",
      "Sample_submitter_city: San Francisco,CA,94143,USA\n",
      "\n",
      "Sample_submitter_department: Comprehensive Cancer Center\n",
      "\n",
      "Sample_submitter_email: albertson@cc.ucsf.edu\n",
      "\n",
      "Sample_submitter_institute: University of California San Francisco\n",
      "\n",
      "Sample_submitter_name: Donna,G,Albertson\n",
      "\n",
      "Sample_submitter_phone: 415 502-8463\n",
      "\n",
      "Sample_target_source1: Cell line GM05296\n",
      "\n",
      "Sample_target_source2: normal male reference genomic DNA\n",
      "\n",
      "Sample_title: CGH_Albertson_GM05296-001218\n",
      "\n",
      "Sample_type: dual channel genomic\n",
      "\n",
      "Column Header Definitions\n",
      "    ID_REF: Unique row identifier, genome position o\n",
      "    rder\n",
      "\n",
      "    LINEAR_RATIO: Mean of replicate Cy3/Cy5 ratios\n",
      "\n",
      "    LOG2STDDEV: Standard deviation of VALUE\n",
      "\n",
      "    NO_REPLICATES: Number of replicate spot measurements\n",
      "\n",
      "    VALUE: aka LOG2RATIO, mean of log base 2 of LIN\n",
      "    EAR_RATIO\n",
      "\n",
      "0: ID_REF\tVALUE\tLINEAR_RATIO\tLOG2STDDEV\tNO_REPLICATES\t\n",
      "1: 1\t\t1.047765\t0.011853\t3\t\n",
      "2: 2\t\t\t\t0\t\n",
      "3: 3\t0.008824\t1.006135\t0.00143\t3\t\n",
      "4: 4\t-0.000894\t0.99938\t0.001454\t3\t\n",
      "5: 5\t0.075875\t1.054\t0.003077\t3\t\n",
      "6: 6\t0.017303\t1.012066\t0.005876\t2\t\n",
      "7: 7\t-0.006766\t0.995321\t0.013881\t3\t\n",
      "8: 8\t0.020755\t1.014491\t0.005506\t3\t\n",
      "9: 9\t-0.094938\t0.936313\t0.012662\t3\t\n",
      "10: 10\t-0.054527\t0.96291\t0.01073\t3\t\n",
      "11: 11\t-0.025057\t0.982782\t0.003855\t3\t\n",
      "12: 12\t\t\t\t0\t\n",
      "13: 13\t0.108454\t1.078072\t0.005196\t3\t\n",
      "14: 14\t0.078633\t1.056017\t0.009165\t3\t\n",
      "15: 15\t0.098571\t1.070712\t0.007834\t3\t\n",
      "16: 16\t0.044048\t1.031003\t0.013651\t3\t\n",
      "17: 17\t0.018039\t1.012582\t0.005471\t3\t\n",
      "18: 18\t-0.088807\t0.9403\t0.010571\t3\t\n",
      "19: 19\t0.016349\t1.011397\t0.007113\t3\t\n",
      "20: 20\t0.030977\t1.021704\t0.016798\t3\t\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from Bio import Geo\n",
    "handle = open(\"data/GSE16.txt\")\n",
    "records = Geo.parse(handle)\n",
    "for record in records:\n",
    "    print(record)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "You can search the “gds” database (GEO datasets) with ESearch:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'27'"
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\" # Always tell NCBI who you are\n",
    "handle = Entrez.esearch(db=\"gds\", term=\"GSE16\")\n",
    "record = Entrez.read(handle)\n",
    "record[\"Count\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['200000016', '100000028', '300000818', '300000817', '300000816', '300000815', '300000814', '300000813', '300000812', '300000811', '300000810', '300000809', '300000808', '300000807', '300000806', '300000805', '300000804', '300000803', '300000802', '300000801']"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"IdList\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "From the Entrez website, UID “200000016” is GDS16 while the other hit\n",
    "“100000028” is for the associated platform, GPL28. Unfortunately, at the\n",
    "time of writing the NCBI don’t seem to support downloading GEO files\n",
    "using Entrez (not as XML, nor in the *Simple Omnibus Format in Text*\n",
    "(SOFT) format).\n",
    "\n",
    "However, it is actually pretty straight forward to download the GEO\n",
    "files by FTP or HTTP from [http://ftp.ncbi.nih.gov/pub/geo/](http://ftp.ncbi.nih.gov/pub/geo/) instead. In this\n",
    "case you might want\n",
    "[http://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE16/GSE16_family.soft.gz](http://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE16/GSE16_family.soft.gz)\n",
    "(a compressed file, see the Python module gzip).\n",
    "\n",
    "### Parsing UniGene records\n",
    "\n",
    "UniGene is an NCBI database of the transcriptome, with each UniGene\n",
    "record showing the set of transcripts that are associated with a\n",
    "particular gene in a specific organism. A typical UniGene record looks\n",
    "like this:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "ID          Hs.2\n",
    "TITLE       N-acetyltransferase 2 (arylamine N-acetyltransferase)\n",
    "GENE        NAT2\n",
    "CYTOBAND    8p22\n",
    "GENE_ID     10\n",
    "LOCUSLINK   10\n",
    "HOMOL       YES\n",
    "EXPRESS      bone| connective tissue| intestine| liver| liver tumor| normal| soft tissue/muscle tissue tumor| adult\n",
    "RESTR_EXPR   adult\n",
    "CHROMOSOME  8\n",
    "STS         ACC=PMC310725P3 UNISTS=272646\n",
    "STS         ACC=WIAF-2120 UNISTS=44576\n",
    "STS         ACC=G59899 UNISTS=137181\n",
    "...\n",
    "STS         ACC=GDB:187676 UNISTS=155563\n",
    "PROTSIM     ORG=10090; PROTGI=6754794; PROTID=NP_035004.1; PCT=76.55; ALN=288\n",
    "PROTSIM     ORG=9796; PROTGI=149742490; PROTID=XP_001487907.1; PCT=79.66; ALN=288\n",
    "PROTSIM     ORG=9986; PROTGI=126722851; PROTID=NP_001075655.1; PCT=76.90; ALN=288\n",
    "...\n",
    "PROTSIM     ORG=9598; PROTGI=114619004; PROTID=XP_519631.2; PCT=98.28; ALN=288\n",
    "\n",
    "SCOUNT      38\n",
    "SEQUENCE    ACC=BC067218.1; NID=g45501306; PID=g45501307; SEQTYPE=mRNA\n",
    "SEQUENCE    ACC=NM_000015.2; NID=g116295259; PID=g116295260; SEQTYPE=mRNA\n",
    "SEQUENCE    ACC=D90042.1; NID=g219415; PID=g219416; SEQTYPE=mRNA\n",
    "SEQUENCE    ACC=D90040.1; NID=g219411; PID=g219412; SEQTYPE=mRNA\n",
    "SEQUENCE    ACC=BC015878.1; NID=g16198419; PID=g16198420; SEQTYPE=mRNA\n",
    "SEQUENCE    ACC=CR407631.1; NID=g47115198; PID=g47115199; SEQTYPE=mRNA\n",
    "SEQUENCE    ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:4722596; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214\n",
    "...\n",
    "SEQUENCE    ACC=AU099534.1; NID=g13550663; CLONE=HSI08034; END=5'; LID=8800; SEQTYPE=EST\n",
    "//\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "This particular record shows the set of transcripts (shown in the\n",
    "`SEQUENCE` lines) that originate from the human gene NAT2, encoding en\n",
    "N-acetyltransferase. The `PROTSIM` lines show proteins with significant\n",
    "similarity to NAT2, whereas the `STS` lines show the corresponding\n",
    "sequence-tagged sites in the genome.\n",
    "\n",
    "To parse UniGene files, use the `Bio.UniGene` module:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<font color='red'>TODO: Need a working example</font>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# from Bio import UniGene\n",
    "# input = open(\"data/myunigenefile.data\")\n",
    "# record = UniGene.read(input)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The `record` returned by `UniGene.read` is a Python object with\n",
    "attributes corresponding to the fields in the UniGene record. For\n",
    "example,\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# record.ID"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# record.title"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The `EXPRESS` and `RESTR_EXPR` lines are stored as Python lists of\n",
    "strings:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "['bone', 'connective tissue', 'intestine', 'liver', 'liver tumor', 'normal', 'soft tissue/muscle tissue tumor', 'adult']\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Specialized objects are returned for the `STS`, `PROTSIM`, and\n",
    "`SEQUENCE` lines, storing the keys shown in each line as attributes:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# record.sts[0].acc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# record.sts[0].unists"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "and similarly for the `PROTSIM` and `SEQUENCE` lines.\n",
    "\n",
    "To parse a file containing more than one UniGene record, use the `parse`\n",
    "function in `Bio.UniGene`:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<font color='red'>TODO: Need a working example</font>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# from Bio import UniGene\n",
    "# input = open(\"unigenerecords.data\")\n",
    "# records = UniGene.parse(input)\n",
    "# for record in records:\n",
    "#     print(record.ID)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Using a proxy\n",
    "-------------\n",
    "\n",
    "Normally you won’t have to worry about using a proxy, but if this is an\n",
    "issue on your network here is how to deal with it. Internally,\n",
    "`Bio.Entrez` uses the standard Python library `urllib` for accessing the\n",
    "NCBI servers. This will check an environment variable called\n",
    "`http_proxy` to configure any simple proxy automatically. Unfortunately\n",
    "this module does not support the use of proxies which require\n",
    "authentication.\n",
    "\n",
    "You may choose to set the `http_proxy` environment variable once (how\n",
    "you do this will depend on your operating system). Alternatively you can\n",
    "set this within Python at the start of your script, for example:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "import os\n",
    "os.environ[\"http_proxy\"] = \"http://proxyhost.example.com:8080\"\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "See the [urllib\n",
    "documentation](http://www.python.org/doc/lib/module-urllib.html) for\n",
    "more details.\n",
    "\n",
    "## Examples\n",
    "\n",
    "### PubMed and Medline {#subsec:pub_med}\n",
    "\n",
    "If you are in the medical field or interested in human issues (and many\n",
    "times even if you are not!), PubMed\n",
    "(<http://www.ncbi.nlm.nih.gov/PubMed/>) is an excellent source of all\n",
    "kinds of goodies. So like other things, we’d like to be able to grab\n",
    "information from it and use it in Python scripts.\n",
    "\n",
    "In this example, we will query PubMed for all articles having to do with\n",
    "orchids (see section \\[sec:orchids\\] for our motivation). We first check\n",
    "how many of such articles there are:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1376\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.egquery(term=\"orchid\")\n",
    "record = Entrez.read(handle)\n",
    "for row in record[\"eGQueryResult\"]:\n",
    "    if row[\"DbName\"]==\"pubmed\":\n",
    "        print(row[\"Count\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Now we use the `Bio.Entrez.efetch` function to download the PubMed IDs\n",
    "of these 463 articles:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The first 10 Id's containing all of the PubMed IDs of articles related to orchids:\n",
      " ['26752741', '26743923', '26738548', '26732875', '26732614', '26724929', '26715121', '26713612', '26708054', '26694378']\n"
     ]
    }
   ],
   "source": [
    "handle = Entrez.esearch(db=\"pubmed\", term=\"orchid\", retmax=463)\n",
    "record = Entrez.read(handle)\n",
    "idlist = record[\"IdList\"]\n",
    "print(\"The first 10 Id's containing all of the PubMed IDs of articles related to orchids:\\n {}\".format(idlist[:10]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Now that we’ve got them, we obviously want to get the corresponding\n",
    "Medline records and extract the information from them. Here, we’ll\n",
    "download the Medline records in the Medline flat-file format, and use\n",
    "the `Bio.Medline` module to parse them:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from Bio import Medline\n",
    "handle = Entrez.efetch(db=\"pubmed\", id=idlist, rettype=\"medline\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "records = Medline.parse(handle)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "NOTE - We’ve just done a separate search and fetch here, the NCBI much\n",
    "prefer you to take advantage of their history support in this situation.\n",
    "See Section [History and WebEnv](#Using-the-history-and-WebEnv).\n",
    "\n",
    "Keep in mind that `records` is an iterator, so you can iterate through\n",
    "the records only once. If you want to save the records, you can convert\n",
    "them to a list:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "records = list(records)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Let’s now iterate over the records to print out some information about\n",
    "each record:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "title: Promise and Challenge of DNA Barcoding in Venus Slipper (Paphiopedilum).\n",
      "authors: ['Guo YY', 'Huang LQ', 'Liu ZJ', 'Wang XQ']\n",
      "source: PLoS One. 2016 Jan 11;11(1):e0146880. doi: 10.1371/journal.pone.0146880. eCollection 2016.\n",
      "\n",
      "title: In vitro profiling of anti-MRSA activity of thymoquinone against selected type and clinical strains.\n",
      "authors: ['Hariharan P', 'Paul-Satyaseela M', 'Gnanamani A']\n",
      "source: Lett Appl Microbiol. 2016 Jan 7. doi: 10.1111/lam.12544.\n",
      "\n",
      "title: Low glutathione redox state couples with a decreased ascorbate redox ratio to accelerate flowering in Oncidium orchid.\n",
      "authors: ['Chin DC', 'Hsieh CC', 'Lin HY', 'Yeh KW']\n",
      "source: Plant Cell Physiol. 2016 Jan 6. pii: pcv206.\n",
      "\n",
      "title: Proteomic and morphometric study of the in vitro interaction between Oncidium sphacelatum Lindl. (Orchidaceae) and Thanatephorus sp. RG26 (Ceratobasidiaceae).\n",
      "authors: ['Lopez-Chavez MY', 'Guillen-Navarro K', 'Bertolini V', 'Encarnacion S', 'Hernandez-Ortiz M', 'Sanchez-Moreno I', 'Damon A']\n",
      "source: Mycorrhiza. 2016 Jan 6.\n",
      "\n",
      "title: A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb.\n",
      "authors: ['Meng Y', 'Yu D', 'Xue J', 'Lu J', 'Feng S', 'Shen C', 'Wang H']\n",
      "source: Sci Rep. 2016 Jan 6;6:18864. doi: 10.1038/srep18864.\n",
      "\n",
      "title: Methods for genetic transformation in Dendrobium.\n",
      "authors: ['Teixeira da Silva JA', 'Dobranszki J', 'Cardoso JC', 'Chandler SF', 'Zeng S']\n",
      "source: Plant Cell Rep. 2016 Jan 2.\n",
      "\n",
      "title: Sebacina vermifera: a unique root symbiont with vast agronomic potential.\n",
      "authors: ['Ray P', 'Craven KD']\n",
      "source: World J Microbiol Biotechnol. 2016 Jan;32(1):16. doi: 10.1007/s11274-015-1970-7. Epub 2015 Dec 29.\n",
      "\n",
      "title: Cuticular Hydrocarbons of Orchid Bees Males: Interspecific and Chemotaxonomy Variation.\n",
      "authors: ['Dos Santos AB', 'do Nascimento FS']\n",
      "source: PLoS One. 2015 Dec 29;10(12):e0145070. doi: 10.1371/journal.pone.0145070. eCollection 2015.\n",
      "\n",
      "title: Sex and the Catasetinae (Darwin's favourite orchids).\n",
      "authors: ['Perez-Escobar OA', 'Gottschling M', 'Whitten WM', 'Salazar G', 'Gerlach G']\n",
      "source: Mol Phylogenet Evol. 2015 Dec 17. pii: S1055-7903(15)00372-3. doi: 10.1016/j.ympev.2015.11.019.\n",
      "\n",
      "title: Comparative Transcriptome Analysis of Genes Involved in GA-GID1-DELLA Regulatory Module in Symbiotic and Asymbiotic Seed Germination of Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae).\n",
      "authors: ['Liu SS', 'Chen J', 'Li SC', 'Zeng X', 'Meng ZX', 'Guo SX']\n",
      "source: Int J Mol Sci. 2015 Dec 18;16(12):30190-203. doi: 10.3390/ijms161226224.\n",
      "\n",
      "title: Dual Drug Loaded Nanoliposomal Chemotherapy: A Promising Strategy for Treatment of Head and Neck Squamous Cell Carcinoma.\n",
      "authors: ['Mohan A', 'Narayanan S', 'Balasubramanian G', 'Sethuraman S', 'Krishnan UM']\n",
      "source: Eur J Pharm Biopharm. 2015 Dec 9. pii: S0939-6411(15)00489-0. doi: 10.1016/j.ejpb.2015.11.017.\n",
      "\n",
      "title: Orally available stilbene derivatives as potent HDAC inhibitors with antiproliferative activities and antitumor effects in human tumor xenografts.\n",
      "authors: ['Kachhadia V', 'Rajagopal S', 'Ponpandian T', 'Vignesh R', 'Anandhan K', 'Prabhu D', 'Rajendran P', 'Nidhyanandan S', 'Roy AM', 'Ahamed FA', 'Surendran N', 'Rajagopal S', 'Narayanan S', 'Gopalan B']\n",
      "source: Eur J Med Chem. 2015 Nov 19;108:274-286. doi: 10.1016/j.ejmech.2015.11.014.\n",
      "\n",
      "title: Parapheromones for Thynnine Wasps.\n",
      "authors: ['Bohman B', 'Karton A', 'Dixon RC', 'Barrow RA', 'Peakall R']\n",
      "source: J Chem Ecol. 2015 Dec 14.\n",
      "\n",
      "title: Interaction networks and the use of floral resources by male orchid bees (Hymenoptera: Apidae: Euglossini) in a primary rain forests of the Choco Region (Colombia).\n",
      "authors: ['Ospina-Torres R', 'Montoya-Pfeiffer PM', 'Parra-H A', 'Solarte V', 'Tupac Otero J']\n",
      "source: Rev Biol Trop. 2015 Sep;63(3):647-58.\n",
      "\n",
      "title: A taste of pineapple evolution through genome sequencing.\n",
      "authors: ['Xu Q', 'Liu ZJ']\n",
      "source: Nat Genet. 2015 Dec 1;47(12):1374-6. doi: 10.1038/ng.3450.\n",
      "\n",
      "title: Somatic Embryogenesis in Two Orchid Genera (Cymbidium, Dendrobium).\n",
      "authors: ['Teixeira da Silva JA', 'Winarto B']\n",
      "source: Methods Mol Biol. 2016;1359:371-86. doi: 10.1007/978-1-4939-3061-6_18.\n",
      "\n",
      "title: Tumors of the Testis: Morphologic Features and Molecular Alterations.\n",
      "authors: ['Howitt BE', 'Berney DM']\n",
      "source: Surg Pathol Clin. 2015 Dec;8(4):687-716. doi: 10.1016/j.path.2015.07.007.\n",
      "\n",
      "title: Scent emission profiles from Darwin's orchid - Angraecum sesquipedale: Investigation of the aldoxime metabolism using clustering analysis.\n",
      "authors: ['Nielsen LJ', 'Moller BL']\n",
      "source: Phytochemistry. 2015 Dec;120:3-18. doi: 10.1016/j.phytochem.2015.10.004. Epub 2015 Oct 22.\n",
      "\n",
      "title: Two common species dominate the species-rich Euglossine bee fauna of an Atlantic Rainforest remnant in Pernambuco, Brazil.\n",
      "authors: ['Oliveira R', 'Pinto CE', 'Schlindwein C']\n",
      "source: Braz J Biol. 2015 Nov;75(4 Suppl 1):1-8. doi: 10.1590/1519-6984.18513. Epub 2015 Nov 24.\n",
      "\n",
      "title: Variation in the Abundance of Neotropical Bees in an Unpredictable Seasonal Environment.\n",
      "authors: ['Knoll FR']\n",
      "source: Neotrop Entomol. 2015 Nov 23.\n",
      "\n",
      "title: Digital Gene Expression Analysis Based on De Novo Transcriptome Assembly Reveals New Genes Associated with Floral Organ Differentiation of the Orchid Plant Cymbidium ensifolium.\n",
      "authors: ['Yang F', 'Zhu G']\n",
      "source: PLoS One. 2015 Nov 18;10(11):e0142434. doi: 10.1371/journal.pone.0142434. eCollection 2015.\n",
      "\n",
      "title: LONG-TERM CONSERVATION OF PROTOCORMS OF Brassavola nodosa (L) LIND. (ORCHIDACEAE): EFFECT OF ABA AND A RANGE OF CRYOCONSERVATION TECHNIQUES.\n",
      "authors: ['Mata-Rosas M', 'Lastre-Puertos E']\n",
      "source: Cryo Letters. 2015 Sep-Oct;36(5):289-98.\n",
      "\n",
      "title: Cuticular Hydrocarbons as Potential Close Range Recognition Cues in Orchid Bees.\n",
      "authors: ['Pokorny T', 'Ramirez SR', 'Weber MG', 'Eltz T']\n",
      "source: J Chem Ecol. 2015 Dec;41(12):1080-94. doi: 10.1007/s10886-015-0647-x. Epub 2015 Nov 14.\n",
      "\n",
      "title: Bilobate leaves of Bauhinia (Leguminosae, Caesalpinioideae, Cercideae) from the middle Miocene of Fujian Province, southeastern China and their biogeographic implications.\n",
      "authors: ['Lin Y', 'Wong WO', 'Shi G', 'Shen S', 'Li Z']\n",
      "source: BMC Evol Biol. 2015 Nov 16;15(1):252. doi: 10.1186/s12862-015-0540-9.\n",
      "\n",
      "title: Functional Significance of Labellum Pattern Variation in a Sexually Deceptive Orchid (Ophrys heldreichii): Evidence of Individual Signature Learning Effects.\n",
      "authors: ['Stejskal K', 'Streinzer M', 'Dyer A', 'Paulus HF', 'Spaethe J']\n",
      "source: PLoS One. 2015 Nov 16;10(11):e0142971. doi: 10.1371/journal.pone.0142971. eCollection 2015.\n",
      "\n",
      "title: Centralization of cleft care in the UK. Part 6: a tale of two studies.\n",
      "authors: ['Ness AR', 'Wills AK', 'Waylen A', 'Al-Ghatam R', 'Jones TE', 'Preston R', 'Ireland AJ', 'Persson M', 'Smallridge J', 'Hall AJ', 'Sell D', 'Sandy JR']\n",
      "source: Orthod Craniofac Res. 2015 Nov;18 Suppl 2:56-62. doi: 10.1111/ocr.12111.\n",
      "\n",
      "title: The Cleft Care UK study. Part 4: perceptual speech outcomes.\n",
      "authors: ['Sell D', 'Mildinhall S', 'Albery L', 'Wills AK', 'Sandy JR', 'Ness AR']\n",
      "source: Orthod Craniofac Res. 2015 Nov;18 Suppl 2:36-46. doi: 10.1111/ocr.12112.\n",
      "\n",
      "title: A cross-sectional survey of 5-year-old children with non-syndromic unilateral cleft lip and palate: the Cleft Care UK study. Part 1: background and methodology.\n",
      "authors: ['Persson M', 'Sandy JR', 'Waylen A', 'Wills AK', 'Al-Ghatam R', 'Ireland AJ', 'Hall AJ', 'Hollingworth W', 'Jones T', 'Peters TJ', 'Preston R', 'Sell D', 'Smallridge J', 'Worthington H', 'Ness AR']\n",
      "source: Orthod Craniofac Res. 2015 Nov;18 Suppl 2:1-13. doi: 10.1111/ocr.12104.\n",
      "\n",
      "title: Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries.\n",
      "authors: ['Kim HT', 'Kim JS', 'Moore MJ', 'Neubig KM', 'Williams NH', 'Whitten WM', 'Kim JH']\n",
      "source: PLoS One. 2015 Nov 11;10(11):e0142215. doi: 10.1371/journal.pone.0142215. eCollection 2015.\n",
      "\n",
      "title: Orchid Species Richness along Elevational and Environmental Gradients in Yunnan, China.\n",
      "authors: ['Zhang SB', 'Chen WY', 'Huang JL', 'Bi YF', 'Yang XF']\n",
      "source: PLoS One. 2015 Nov 10;10(11):e0142621. doi: 10.1371/journal.pone.0142621. eCollection 2015.\n",
      "\n",
      "title: Severe outbreeding and inbreeding depression maintain mating system differentiation in Epipactis (Orchidaceae).\n",
      "authors: ['Brys R', 'Jacquemyn H']\n",
      "source: J Evol Biol. 2015 Nov 9. doi: 10.1111/jeb.12787.\n",
      "\n",
      "title: Simultaneous detection of Cymbidium mosaic virus and Odontoglossum ringspot virus in orchids using multiplex RT-PCR.\n",
      "authors: ['Kim SM', 'Choi SH']\n",
      "source: Virus Genes. 2015 Dec;51(3):417-22. doi: 10.1007/s11262-015-1258-x. Epub 2015 Nov 5.\n",
      "\n",
      "title: Analysis of the TCP genes expressed in the inflorescence of the orchid Orchis italica.\n",
      "authors: ['De Paolo S', 'Gaudio L', 'Aceto S']\n",
      "source: Sci Rep. 2015 Nov 4;5:16265. doi: 10.1038/srep16265.\n",
      "\n",
      "title: RNA-Seq SSRs of Moth Orchid and Screening for Molecular Markers across Genus Phalaenopsis (Orchidaceae).\n",
      "authors: ['Tsai CC', 'Shih HC', 'Wang HV', 'Lin YS', 'Chang CH', 'Chiang YC', 'Chou CH']\n",
      "source: PLoS One. 2015 Nov 2;10(11):e0141761. doi: 10.1371/journal.pone.0141761. eCollection 2015.\n",
      "\n",
      "title: Mapping Adolescent Cancer Services: How Do Young People, Their Families, and Staff Describe Specialized Cancer Care in England?\n",
      "authors: ['Vindrola-Padros C', 'Taylor RM', 'Lea S', 'Hooker L', 'Pearce S', 'Whelan J', 'Gibson F']\n",
      "source: Cancer Nurs. 2015 Oct 28.\n",
      "\n",
      "title: A putative miR172-targeted CeAPETALA2-like gene is involved in floral patterning regulation of the orchid Cymbidium ensifolium.\n",
      "authors: ['Yang FX', 'Zhu GF', 'Wang Z', 'Liu HL', 'Huang D']\n",
      "source: Genet Mol Res. 2015 Oct 5;14(4):12049-61. doi: 10.4238/2015.October.5.18.\n",
      "\n",
      "title: Functional Characterization of PhapLEAFY, a FLORICAULA/LEAFY Ortholog in Phalaenopsis aphrodite.\n",
      "authors: ['Jang S']\n",
      "source: Plant Cell Physiol. 2015 Nov;56(11):2234-47. doi: 10.1093/pcp/pcv130. Epub 2015 Oct 22.\n",
      "\n",
      "title: Evolutionary history of PEPC genes in green plants: Implications for the evolution of CAM in orchids.\n",
      "authors: ['Deng H', 'Zhang LS', 'Zhang GQ', 'Zheng BQ', 'Liu ZJ', 'Wang Y']\n",
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      "\n",
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      "\n",
      "title: Asymbiotic seed germination and in vitro conservation of Coelogyne nervosa A. Rich. an endemic orchid to Western Ghats.\n",
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      "source: Physiol Mol Biol Plants. 2012 Jul;18(3):245-51. doi: 10.1007/s12298-012-0118-6.\n",
      "\n",
      "title: Endophytic and mycorrhizal fungi associated with roots of endangered native orchids from the Atlantic Forest, Brazil.\n",
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      "\n",
      "title: Convergent evolution of floral signals underlies the success of Neotropical orchids.\n",
      "authors: ['Papadopulos AS', 'Powell MP', 'Pupulin F', 'Warner J', 'Hawkins JA', 'Salamin N', 'Chittka L', 'Williams NH', 'Whitten WM', 'Loader D', 'Valente LM', 'Chase MW', 'Savolainen V']\n",
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      "\n",
      "title: 3,3'-{[(Biphenyl-2,2'-di-yl)bis-(methyl-ene)]bis-(-oxy)}bis-[N-(4-chloro-phen-yl) benzamide].\n",
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      "\n",
      "title: 3,5-Dimethyl-1-{2-[(5-methyl-1,3,4-thia-diazol-2-yl)sulfan-yl]acet-yl}-2,6-diphen ylpiperidin-4-one.\n",
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      "\n",
      "title: Symbiotic seed germination and protocorm development of Aa achalensis Schltr., a terrestrial orchid endemic from Argentina.\n",
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      "\n",
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      "\n",
      "title: Detection of viruses directly from the fresh leaves of a Phalaenopsis orchid using a microfluidic system.\n",
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      "source: Nanomedicine. 2013 Nov;9(8):1274-82. doi: 10.1016/j.nano.2013.05.016. Epub 2013 Jun 8.\n",
      "\n",
      "title: Floral visual signal increases reproductive success in a sexually deceptive orchid.\n",
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      "\n",
      "title: Moscatilin inhibits lung cancer cell motility and invasion via suppression of endogenous reactive oxygen species.\n",
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      "\n",
      "title: Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids.\n",
      "authors: ['Sedeek KE', 'Qi W', 'Schauer MA', 'Gupta AK', 'Poveda L', 'Xu S', 'Liu ZJ', 'Grossniklaus U', 'Schiestl FP', 'Schluter PM']\n",
      "source: PLoS One. 2013 May 29;8(5):e64621. doi: 10.1371/journal.pone.0064621. Print 2013.\n",
      "\n",
      "title: Beyond orchids and dandelions: testing the 5-HTT \"risky\" allele for evidence of phenotypic capacitance and frequency-dependent selection.\n",
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      "\n",
      "title: Molecular cloning and spatiotemporal expression of an APETALA1/FRUITFULL-like MADS-box gene from the orchid (Cymbidium faberi).\n",
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      "\n",
      "title: Antigenotoxic effect, composition and antioxidant activity of Dendrobium speciosum.\n",
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      "\n",
      "title: Exposure to HIV prevention programmes associated with improved condom use and uptake of HIV testing by female sex workers in Nagaland, Northeast India.\n",
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      "\n",
      "title: Significant spatial aggregation and fine-scale genetic structure in the homosporous fern Cyrtomium falcatum (Dryopteridaceae).\n",
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      "\n",
      "title: Catalase and superoxide dismutase activities and the total protein content of protocorm-like bodies of Dendrobium sonia-28 subjected to vitrification.\n",
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      "\n",
      "title: Organ homologies in orchid flowers re-interpreted using the Musk Orchid as a model.\n",
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      "source: PeerJ. 2013 Feb 12;1:e26. doi: 10.7717/peerj.26. Print 2013.\n",
      "\n",
      "title: Accessing local knowledge to identify where species of conservation concern occur in a tropical forest landscape.\n",
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      "\n",
      "title: Spatial patterns of photosynthesis in thin- and thick-leaved epiphytic orchids: unravelling C3-CAM plasticity in an organ-compartmented way.\n",
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      "\n",
      "title: Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development.\n",
      "authors: ['Zhang J', 'Wu K', 'Zeng S', 'Teixeira da Silva JA', 'Zhao X', 'Tian CE', 'Xia H', 'Duan J']\n",
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      "\n",
      "title: Orchid fleck virus structural proteins N and P form intranuclear viroplasm-like structures in the absence of viral infection.\n",
      "authors: ['Kondo H', 'Chiba S', 'Andika IB', 'Maruyama K', 'Tamada T', 'Suzuki N']\n",
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      "\n",
      "title: Scale-up of a comprehensive harm reduction programme for people injecting opioids: lessons from north-eastern India.\n",
      "authors: ['Lalmuanpuii M', 'Biangtung L', 'Mishra RK', 'Reeve MJ', 'Tzudier S', 'Singh AL', 'Sinate R', 'Sgaier SK']\n",
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      "\n",
      "title: Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses.\n",
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      "source: BMC Evol Biol. 2013 Apr 18;13:84. doi: 10.1186/1471-2148-13-84.\n",
      "\n",
      "title: A novel aphrodisiac compound from an orchid that activates nitric oxide synthases.\n",
      "authors: ['Subramoniam A', 'Gangaprasad A', 'Sureshkumar PK', 'Radhika J', 'Arun KB']\n",
      "source: Int J Impot Res. 2013 Nov-Dec;25(6):212-6. doi: 10.1038/ijir.2013.18. Epub 2013 Apr 18.\n",
      "\n",
      "title: A new orchid genus, Danxiaorchis, and phylogenetic analysis of the tribe Calypsoeae.\n",
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      "\n",
      "title: Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population.\n",
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      "\n",
      "title: A new molecular phylogeny and a new genus, Pendulorchis, of the Aerides-Vanda alliance (Orchidaceae: Epidendroideae).\n",
      "authors: ['Zhang GQ', 'Liu KW', 'Chen LJ', 'Xiao XJ', 'Zhai JW', 'Li LQ', 'Cai J', 'Hsiao YY', 'Rao WH', 'Huang J', 'Ma XY', 'Chung SW', 'Huang LQ', 'Tsai WC', 'Liu ZJ']\n",
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      "\n",
      "title: Catalog of Erycina pusilla miRNA and categorization of reproductive phase-related miRNAs and their target gene families.\n",
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      "\n",
      "title: The rare terrestrial orchid Nervilia nipponica consistently associates with a single group of novel mycobionts.\n",
      "authors: ['Nomura N', 'Ogura-Tsujita Y', 'Gale SW', 'Maeda A', 'Umata H', 'Hosaka K', 'Yukawa T']\n",
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      "\n",
      "title: Compatible fungi, suitable medium, and appropriate developmental stage essential for stable association of Dendrobium chrysanthum.\n",
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      "\n",
      "title: The host bias of three epiphytic Aeridinae orchid species is reflected, but not explained, by mycorrhizal fungal associations.\n",
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      "\n",
      "title: Microsatellite markers in the western prairie fringed orchid, Platanthera praeclara (Orchidaceae).\n",
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      "\n",
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      "\n",
      "title: Mycorrhizas alter nitrogen acquisition by the terrestrial orchid Cymbidium goeringii.\n",
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      "\n",
      "title: Variation in nutrient-acquisition patterns by mycorrhizal fungi of rare and common orchids explains diversification in a global biodiversity hotspot.\n",
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      "\n",
      "title: Bioanalytical method development, validation and quantification of dorsomorphin in rat plasma by LC-MS/MS.\n",
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      "title: Cryopreservation of orchid mycorrhizal fungi: a tool for the conservation of endangered species.\n",
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      "\n",
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      "title: Ascertaining the role of Taiwan as a source for the Austronesian expansion.\n",
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      "\n",
      "title: Acquisition of species-specific perfume blends: influence of habitat-dependent compound availability on odour choices of male orchid bees (Euglossa spp.).\n",
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      "title: A narrowly endemic photosynthetic orchid is non-specific in its mycorrhizal associations.\n",
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      "\n",
      "title: Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla.\n",
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      "title: Overexpression of DOSOC1, an ortholog of Arabidopsis SOC1, promotes flowering in the orchid Dendrobium Chao Parya Smile.\n",
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      "\n",
      "title: SPAR methods revealed high genetic diversity within populations and high gene flow of Vanda coerulea Griff ex Lindl (Blue Vanda), an endangered orchid species.\n",
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      "title: Oriental orchid (Cymbidium floribundum) attracts the Japanese honeybee (Apis cerana japonica) with a mixture of 3-hydroxyoctanoic acid and 10-hydroxy- (E)-2-decenoic acid.\n",
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      "title: Marital satisfaction and physical health: evidence for an orchid effect.\n",
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      "title: Fungal host specificity is not a bottleneck for the germination of Pyroleae species (Ericaceae) in a Bavarian forest.\n",
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      "\n",
      "title: First Report of Sclerotium Rot on Cymbidium Orchids Caused by Sclerotium rolfsii in Korea.\n",
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      "title: OrchidBase 2.0: comprehensive collection of Orchidaceae floral transcriptomes.\n",
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      "\n",
      "title: Adding perches for cross-pollination ensures the reproduction of a self-incompatible orchid.\n",
      "authors: ['Liu ZJ', 'Chen LJ', 'Liu KW', 'Li LQ', 'Rao WH', 'Zhang YT', 'Tang GD', 'Huang LQ']\n",
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      "\n",
      "title: Aerial roots of epiphytic orchids: the velamen radicum and its role in water and nutrient uptake.\n",
      "authors: ['Zotz G', 'Winkler U']\n",
      "source: Oecologia. 2013 Mar;171(3):733-41. doi: 10.1007/s00442-012-2575-6. Epub 2013 Jan 6.\n",
      "\n",
      "title: The OitaAG and OitaSTK genes of the orchid Orchis italica: a comparative analysis with other C- and D-class MADS-box genes.\n",
      "authors: ['Salemme M', 'Sica M', 'Gaudio L', 'Aceto S']\n",
      "source: Mol Biol Rep. 2013 May;40(5):3523-35. doi: 10.1007/s11033-012-2426-x. Epub 2013 Jan 1.\n",
      "\n",
      "title: Mycorrhizal preference promotes habitat invasion by a native Australian orchid: Microtis media.\n",
      "authors: ['De Long JR', 'Swarts ND', 'Dixon KW', 'Egerton-Warburton LM']\n",
      "source: Ann Bot. 2013 Mar;111(3):409-18. doi: 10.1093/aob/mcs294. Epub 2012 Dec 28.\n",
      "\n",
      "title: [Plant rhabdoviruses with bipartite genomes].\n",
      "authors: ['Kondo H']\n",
      "source: Uirusu. 2013;63(2):143-54.\n",
      "\n",
      "title: Functional characterization of Candida albicans Hos2 histone deacetylase.\n",
      "authors: ['Karthikeyan G', 'Paul-Satyaseela M', 'Dhatchana Moorthy N', 'Gopalaswamy R', 'Narayanan S']\n",
      "source: F1000Res. 2013 Nov 11;2:238. doi: 10.12688/f1000research.2-238.v3. eCollection 2013.\n",
      "\n",
      "title: Eufriesea zhangi sp. n. (Hymenoptera: Apidae: Euglossina), a new orchid bee from Brazil revealed by molecular and morphological characters.\n",
      "authors: ['Nemesio A', 'Junior JE', 'Santos FR']\n",
      "source: Zootaxa. 2013 Feb 4;3609:568-82. doi: 10.11646/zootaxa.3609.6.2.\n",
      "\n",
      "title: Specificity and preference of mycorrhizal associations in two species of the genus Dendrobium (Orchidaceae).\n",
      "authors: ['Xing X', 'Ma X', 'Deng Z', 'Chen J', 'Wu F', 'Guo S']\n",
      "source: Mycorrhiza. 2013 May;23(4):317-24. doi: 10.1007/s00572-012-0473-8. Epub 2012 Dec 28.\n",
      "\n",
      "title: Transcriptomic analysis of floral organs from Phalaenopsis orchid by using oligonucleotide microarray.\n",
      "authors: ['Hsiao YY', 'Huang TH', 'Fu CH', 'Huang SC', 'Chen YJ', 'Huang YM', 'Chen WH', 'Tsai WC', 'Chen HH']\n",
      "source: Gene. 2013 Apr 10;518(1):91-100. doi: 10.1016/j.gene.2012.11.069. Epub 2012 Dec 20.\n",
      "\n",
      "title: mRNA profiling using a minimum of five mRNA markers per body fluid and a novel scoring method for body fluid identification.\n",
      "authors: ['Roeder AD', 'Haas C']\n",
      "source: Int J Legal Med. 2013 Jul;127(4):707-21. doi: 10.1007/s00414-012-0794-3. Epub 2012 Dec 20.\n",
      "\n",
      "title: Monophyly or paraphyly--the taxonomy of Holcoglossum (Aeridinae: Orchidaceae).\n",
      "authors: ['Xiang X', 'Li D', 'Jin X', 'Hu H', 'Zhou H', 'Jin W', 'Lai Y']\n",
      "source: PLoS One. 2012;7(12):e52050. doi: 10.1371/journal.pone.0052050. Epub 2012 Dec 14.\n",
      "\n",
      "title: A comparative study of vitrification and encapsulation-vitrification for cryopreservation of protocorms of Cymbidium eburneum L., a threatened and vulnerable orchid of India.\n",
      "authors: ['Gogoi K', 'Kumaria S', 'Tandon P']\n",
      "source: Cryo Letters. 2012 Nov-Dec;33(6):443-52.\n",
      "\n",
      "title: Understanding the association between injecting and sexual risk behaviors of injecting drug users in Manipur and Nagaland, India.\n",
      "authors: ['Suohu K', 'Humtsoe C', 'Saggurti N', 'Sabarwal S', 'Mahapatra B', 'Kermode M']\n",
      "source: Harm Reduct J. 2012 Dec 18;9:40. doi: 10.1186/1477-7517-9-40.\n",
      "\n",
      "title: A new antibacterial phenanthrenequinone from Dendrobium sinense.\n",
      "authors: ['Chen XJ', 'Mei WL', 'Zuo WJ', 'Zeng YB', 'Guo ZK', 'Song XQ', 'Dai HF']\n",
      "source: J Asian Nat Prod Res. 2013;15(1):67-70. doi: 10.1080/10286020.2012.740473. Epub 2012 Dec 11.\n",
      "\n",
      "title: The Doctrine of Signatures, Materia Medica of Orchids, and the Contributions of Doctor - Orchidologists.\n",
      "authors: ['Pearn J']\n",
      "source: Vesalius. 2012 Dec;18(2):99-106.\n",
      "\n",
      "title: Reference-free comparative genomics of 174 chloroplasts.\n",
      "authors: ['Kua CS', 'Ruan J', 'Harting J', 'Ye CX', 'Helmus MR', 'Yu J', 'Cannon CH']\n",
      "source: PLoS One. 2012;7(11):e48995. doi: 10.1371/journal.pone.0048995. Epub 2012 Nov 20.\n",
      "\n",
      "title: Multiple shoot induction from axillary bud cultures of the medicinal orchid, Dendrobium longicornu.\n",
      "authors: ['Dohling S', 'Kumaria S', 'Tandon P']\n",
      "source: AoB Plants. 2012;2012:pls032. doi: 10.1093/aobpla/pls032. Epub 2012 Nov 5.\n",
      "\n",
      "title: Germination failure is not a critical stage of reproductive isolation between three congeneric orchid species.\n",
      "authors: ['De Hert K', 'Honnay O', 'Jacquemyn H']\n",
      "source: Am J Bot. 2012 Nov;99(11):1884-90. doi: 10.3732/ajb.1200381. Epub 2012 Nov 6.\n",
      "\n",
      "title: Three new cryptic species of Euglossa from Brazil (Hymenoptera, Apidae).\n",
      "authors: ['Nemesio A', 'Engel MS']\n",
      "source: Zookeys. 2012;(222):47-68. doi: 10.3897/zookeys.222.3382. Epub 2012 Sep 21.\n",
      "\n",
      "title: Two new species of Euglossa from South America, with notes on their taxonomic affinities (Hymenoptera, Apidae).\n",
      "authors: ['Hinojosa-Diaz IA', 'Nemesio A', 'Engel MS']\n",
      "source: Zookeys. 2012;(221):63-79. doi: 10.3897/zookeys.221.3659. Epub 2012 Sep 13.\n",
      "\n",
      "title: Genetic variation and structure within 3 endangered Calanthe species (Orchidaceae) from Korea: inference of population-establishment history and implications for conservation.\n",
      "authors: ['Chung MY', 'Lopez-Pujol J', 'Maki M', 'Moon MO', 'Hyun JO', 'Chung MG']\n",
      "source: J Hered. 2013 Mar;104(2):248-62. doi: 10.1093/jhered/ess088. Epub 2012 Nov 1.\n",
      "\n",
      "title: Briacavatolides D-F, new briaranes from the Taiwanese octocoral Briareum excavatum.\n",
      "authors: ['Wang SK', 'Yeh TT', 'Duh CY']\n",
      "source: Mar Drugs. 2012 Sep;10(9):2103-10. doi: 10.3390/md10092103. Epub 2012 Sep 24.\n",
      "\n",
      "title: Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study.\n",
      "authors: ['Lambert SB', 'Ware RS', 'Cook AL', 'Maguire FA', 'Whiley DM', 'Bialasiewicz S', 'Mackay IM', 'Wang D', 'Sloots TP', 'Nissen MD', 'Grimwood K']\n",
      "source: BMJ Open. 2012 Oct 31;2(6). pii: e002134. doi: 10.1136/bmjopen-2012-002134. Print 2012.\n",
      "\n",
      "title: Microsatellite primers for the neotropical epiphyte Epidendrum firmum (Orchidaceae).\n",
      "authors: ['Kartzinel TR', 'Trapnell DW', 'Glenn TC']\n",
      "source: Am J Bot. 2012 Nov;99(11):e450-2. doi: 10.3732/ajb.1200232. Epub 2012 Oct 31.\n",
      "\n",
      "title: The production of a key floral volatile is dependent on UV light in a sexually deceptive orchid.\n",
      "authors: ['Falara V', 'Amarasinghe R', 'Poldy J', 'Pichersky E', 'Barrow RA', 'Peakall R']\n",
      "source: Ann Bot. 2013 Jan;111(1):21-30. doi: 10.1093/aob/mcs228. Epub 2012 Oct 22.\n",
      "\n",
      "title: Exotic and indigenous viruses infect wild populations and captive collections of temperate terrestrial orchids (Diuris species) in Australia.\n",
      "authors: ['Wylie SJ', 'Li H', 'Dixon KW', 'Richards H', 'Jones MG']\n",
      "source: Virus Res. 2013 Jan;171(1):22-32. doi: 10.1016/j.virusres.2012.10.003. Epub 2012 Oct 23.\n",
      "\n",
      "title: Orchid fleck virus: an unclassified bipartite, negative-sense RNA plant virus.\n",
      "authors: ['Peng de W', 'Zheng GH', 'Zheng ZZ', 'Tong QX', 'Ming YL']\n",
      "source: Arch Virol. 2013 Feb;158(2):313-23. doi: 10.1007/s00705-012-1506-5. Epub 2012 Oct 16.\n",
      "\n",
      "title: Untangling above- and belowground mycorrhizal fungal networks in tropical orchids.\n",
      "authors: ['Leake JR', 'Cameron DD']\n",
      "source: Mol Ecol. 2012 Oct;21(20):4921-4. doi: 10.1111/j.1365-294X.2012.05718.x.\n",
      "\n",
      "title: Pre-adaptations and the evolution of pollination by sexual deception: Cope's rule of specialization revisited.\n",
      "authors: ['Vereecken NJ', 'Wilson CA', 'Hotling S', 'Schulz S', 'Banketov SA', 'Mardulyn P']\n",
      "source: Proc Biol Sci. 2012 Dec 7;279(1748):4786-94. doi: 10.1098/rspb.2012.1804. Epub 2012 Oct 10.\n",
      "\n",
      "title: The mirror crack'd: both pigment and structure contribute to the glossy blue appearance of the mirror orchid, Ophrys speculum.\n",
      "authors: ['Vignolini S', 'Davey MP', 'Bateman RM', 'Rudall PJ', 'Moyroud E', 'Tratt J', 'Malmgren S', 'Steiner U', 'Glover BJ']\n",
      "source: New Phytol. 2012 Dec;196(4):1038-47. doi: 10.1111/j.1469-8137.2012.04356.x. Epub 2012 Oct 9.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "for record in records:\n",
    "    print(\"title:\", record.get(\"TI\", \"?\"))\n",
    "    print(\"authors:\", record.get(\"AU\", \"?\"))\n",
    "    print(\"source:\", record.get(\"SO\", \"?\"))\n",
    "    print(\"\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The output for this looks like:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "title: Sex pheromone mimicry in the early spider orchid (ophrys sphegodes):\n",
    "patterns of hydrocarbons as the key mechanism for pollination by sexual\n",
    "deception [In Process Citation]\n",
    "authors: ['Schiestl FP', 'Ayasse M', 'Paulus HF', 'Lofstedt C', 'Hansson BS',\n",
    "'Ibarra F', 'Francke W']\n",
    "source: J Comp Physiol [A] 2000 Jun;186(6):567-74\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Especially interesting to note is the list of authors, which is returned\n",
    "as a standard Python list. This makes it easy to manipulate and search\n",
    "using standard Python tools. For instance, we could loop through a whole\n",
    "bunch of entries searching for a particular author with code like the\n",
    "following:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "search_author = \"Waits T\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "for record in records:\n",
    "    if not \"AU\" in record:\n",
    "        continue\n",
    "    if search_author in record[\"AU\"]:\n",
    "        print(\"Author %s found: %s\" % (search_author, record[\"SO\"]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Hopefully this section gave you an idea of the power and flexibility of\n",
    "the Entrez and Medline interfaces and how they can be used together.\n",
    "\n",
    "### Searching, downloading, and parsing Entrez Nucleotide records {#subsec:entrez_example_genbank}\n",
    "\n",
    "Here we’ll show a simple example of performing a remote Entrez query. In\n",
    "section \\[sec:orchids\\] of the parsing examples, we talked about using\n",
    "NCBI’s Entrez website to search the NCBI nucleotide databases for info\n",
    "on Cypripedioideae, our friends the lady slipper orchids. Now, we’ll\n",
    "look at how to automate that process using a Python script. In this\n",
    "example, we’ll just show how to connect, get the results, and parse\n",
    "them, with the Entrez module doing all of the work.\n",
    "\n",
    "First, we use EGQuery to find out the number of results we will get\n",
    "before actually downloading them. EGQuery will tell us how many search\n",
    "results were found in each of the databases, but for this example we are\n",
    "only interested in nucleotides:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4247\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.egquery(term=\"Cypripedioideae\")\n",
    "record = Entrez.read(handle)\n",
    "for row in record[\"eGQueryResult\"]:\n",
    "    if row[\"DbName\"]==\"nuccore\":\n",
    "        print(row[\"Count\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "So, we expect to find 814 Entrez Nucleotide records (this is the number\n",
    "I obtained in 2008; it is likely to increase in the future). If you find\n",
    "some ridiculously high number of hits, you may want to reconsider if you\n",
    "really want to download all of them, which is our next step:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from Bio import Entrez\n",
    "handle = Entrez.esearch(db=\"nucleotide\", term=\"Cypripedioideae\", retmax=814)\n",
    "record = Entrez.read(handle)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Here, `record` is a Python dictionary containing the search results and\n",
    "some auxiliary information. Just for information, let’s look at what is\n",
    "stored in this dictionary:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dict_keys(['TranslationStack', 'IdList', 'TranslationSet', 'QueryTranslation', 'Count', 'RetStart', 'RetMax'])\n"
     ]
    }
   ],
   "source": [
    "print(record.keys())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "First, let’s check how many results were found:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4247\n"
     ]
    }
   ],
   "source": [
    "print(record[\"Count\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "which is the number we expected. The 814 results are stored in\n",
    "`record['IdList']`:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "814"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(record[\"IdList\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Let’s look at the first five results:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['874509867', '874509089', '844174433', '937957673', '694174838']"
      ]
     },
     "execution_count": 67,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"IdList\"][:5]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "\\[sec:entrez-batched-efetch\\] We can download these records using\n",
    "`efetch`. While you could download these records one by one, to reduce\n",
    "the load on NCBI’s servers, it is better to fetch a bunch of records at\n",
    "the same time, shown below. However, in this situation you should\n",
    "ideally be using the history feature described later in\n",
    "Section [History and WebEnv](#Using-the-history-and-WebEnv).\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "874509867,874509089,844174433,937957673,694174838\n"
     ]
    }
   ],
   "source": [
    "idlist = \",\".join(record[\"IdList\"][:5])\n",
    "print(idlist)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5"
      ]
     },
     "execution_count": 69,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "handle = Entrez.efetch(db=\"nucleotide\", id=idlist, retmode=\"xml\")\n",
    "records = Entrez.read(handle)\n",
    "len(records)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Each of these records corresponds to one GenBank record.\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dict_keys(['GBSeq_division', 'GBSeq_moltype', 'GBSeq_definition', 'GBSeq_topology', 'GBSeq_locus', 'GBSeq_strandedness', 'GBSeq_source', 'GBSeq_taxonomy', 'GBSeq_create-date', 'GBSeq_accession-version', 'GBSeq_references', 'GBSeq_sequence', 'GBSeq_other-seqids', 'GBSeq_primary-accession', 'GBSeq_length', 'GBSeq_update-date', 'GBSeq_feature-table', 'GBSeq_organism'])\n"
     ]
    }
   ],
   "source": [
    "print(records[0].keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "KP644081\n"
     ]
    }
   ],
   "source": [
    "print(records[0][\"GBSeq_primary-accession\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['gnl|uoguelph|SCBI449-14.rbcLa', 'gb|KP644081.1|', 'gi|874509867']\n"
     ]
    }
   ],
   "source": [
    "print(records[0][\"GBSeq_other-seqids\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Cypripedium calceolus voucher SNP_13_0359 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast\n"
     ]
    }
   ],
   "source": [
    "print(records[0][\"GBSeq_definition\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Cypripedium calceolus\n"
     ]
    }
   ],
   "source": [
    "print(records[0][\"GBSeq_organism\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "You could use this to quickly set up searches – but for heavy usage, see\n",
    "Section [History and WebEnv](#Using-the-history-and-WebEnv).\n",
    "\n",
    "### Searching, downloading, and parsing GenBank records {#sec:entrez-search-fetch-genbank}\n",
    "\n",
    "The GenBank record format is a very popular method of holding\n",
    "information about sequences, sequence features, and other associated\n",
    "sequence information. The format is a good way to get information from\n",
    "the NCBI databases at <http://www.ncbi.nlm.nih.gov/>.\n",
    "\n",
    "In this example we’ll show how to query the NCBI databases,to retrieve\n",
    "the records from the query, and then parse them using `Bio.SeqIO` -\n",
    "something touched on in Section \\[sec:SeqIO\\_GenBank\\_Online\\]. For\n",
    "simplicity, this example *does not* take advantage of the WebEnv history\n",
    "feature – see Section [History and WebEnv](#Using-the-history-and-WebEnv) for this.\n",
    "\n",
    "First, we want to make a query and find out the ids of the records to\n",
    "retrieve. Here we’ll do a quick search for one of our favorite\n",
    "organisms, *Opuntia* (prickly-pear cacti). We can do quick search and\n",
    "get back the GIs (GenBank identifiers) for all of the corresponding\n",
    "records. First we check how many records there are:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "26\n"
     ]
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.egquery(term=\"Opuntia AND rpl16\")\n",
    "record = Entrez.read(handle)\n",
    "for row in record[\"eGQueryResult\"]:\n",
    "    if row[\"DbName\"]==\"nuccore\":\n",
    "        print(row[\"Count\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Now we download the list of GenBank identifiers:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['377581039', '330887241', '330887240', '330887239', '330887238', '330887237', '330887236', '330887235', '330887233', '330887232', '330887231', '330887228', '330887227', '330887226', '330887225', '330887224', '330887223', '57240072', '57240071', '6273287']"
      ]
     },
     "execution_count": 76,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "handle = Entrez.esearch(db=\"nuccore\", term=\"Opuntia AND rpl16\")\n",
    "record = Entrez.read(handle)\n",
    "gi_list = record[\"IdList\"]\n",
    "gi_list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Now we use these GIs to download the GenBank records - note that with\n",
    "older versions of Biopython you had to supply a comma separated list of\n",
    "GI numbers to Entrez, as of Biopython 1.59 you can pass a list and this\n",
    "is converted for you:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "gi_str = \",\".join(gi_list)\n",
    "handle = Entrez.efetch(db=\"nuccore\", id=gi_str, rettype=\"gb\", retmode=\"text\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "If you want to look at the raw GenBank files, you can read from this\n",
    "handle and print out the result:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LOCUS       HQ621368                 399 bp    DNA     linear   PLN 26-FEB-2012\n",
      "DEFINITION  Opuntia decumbens voucher Martinez & Eggli 146a (ZSS) ribosomal\n",
      "            protein L16 (rpl16) gene, partial cds; chloroplast.\n",
      "ACCESSION   HQ621368\n",
      "VERSION     HQ621368.1  GI:377581039\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia decumbens\n",
      "  ORGANISM  Opuntia decumbens\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 399)\n",
      "  AUTHORS   Arakaki,M., Christin,P.A., Nyffeler,R., Lendel,A., Eggli,U.,\n",
      "            Ogburn,R.M., Spriggs,E., Moore,M.J. and Edwards,E.J.\n",
      "  TITLE     Contemporaneous and recent radiations of the world's major\n",
      "            succulent plant lineages\n",
      "  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 108 (20), 8379-8384 (2011)\n",
      "   PUBMED   21536881\n",
      "REFERENCE   2  (bases 1 to 399)\n",
      "  AUTHORS   Arakaki,M., Christin,P.-A., Nyffeler,R., Eggli,U., Ogburn,R.M.,\n",
      "            Spriggs,E., Moore,M.J. and Edwards,E.J.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (15-NOV-2010) Department of Ecology and Evolutionary\n",
      "            Biology, Brown University, 80 Waterman St., Providence, RI 02912,\n",
      "            USA\n",
      "COMMENT     ##Assembly-Data-START##\n",
      "            Assembly Method       :: MIRA V3rc4; Geneious v. 4.8\n",
      "            Sequencing Technology :: 454\n",
      "            ##Assembly-Data-END##\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..399\n",
      "                     /organism=\"Opuntia decumbens\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /specimen_voucher=\"Martinez & Eggli 146a (ZSS)\"\n",
      "                     /db_xref=\"taxon:867482\"\n",
      "                     /tissue_type=\"stem\"\n",
      "                     /note=\"authority: Opuntia decumbens Salm-Dyck\"\n",
      "     gene            <1..>399\n",
      "                     /gene=\"rpl16\"\n",
      "     CDS             <1..>399\n",
      "                     /gene=\"rpl16\"\n",
      "                     /codon_start=1\n",
      "                     /transl_table=11\n",
      "                     /product=\"ribosomal protein L16\"\n",
      "                     /protein_id=\"AFB70658.1\"\n",
      "                     /db_xref=\"GI:377581040\"\n",
      "                     /translation=\"NPKRTRFCKQHRGRMKGISYRGNRICFGRYALQALEPAWITSRQ\n",
      "                     IEAGRRAMTRNARRGGKIWVRIFPDKPVTVKSAESRMGSGKGSHLYWVVVVKPGRILY\n",
      "                     EISGVSENIARRAISIAASKMPVRTQFIISG\"\n",
      "ORIGIN      \n",
      "        1 aaccccaaaa gaaccagatt ctgtaaacaa catagaggaa gaatgaaggg aatatcttat\n",
      "       61 cgggggaatc gtatttgttt cggaagatat gctcttcagg cacttgagcc tgcttggatc\n",
      "      121 acgtctagac aaatagaagc aggtcggcga gcaatgacgc gaaatgcacg ccgcggtgga\n",
      "      181 aaaatatggg tacgtatatt tccagacaaa ccagttacag taaaatctgc ggaaagccgt\n",
      "      241 atgggttcgg ggaaaggatc ccacctatat tgggtagttg ttgtcaaacc cggtcgaata\n",
      "      301 ctttatgaaa taagcggagt atcagaaaat atagcccgaa gggctatctc gatagcggca\n",
      "      361 tctaaaatgc ctgtacgaac tcaattcatt atttcagga\n",
      "//\n",
      "\n",
      "LOCUS       HM041482                1197 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Cylindropuntia tunicata ribosomal protein L16-like (rpl16) gene,\n",
      "            partial sequence; chloroplast.\n",
      "ACCESSION   HM041482\n",
      "VERSION     HM041482.1  GI:330887241\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Cylindropuntia tunicata\n",
      "  ORGANISM  Cylindropuntia tunicata\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Cylindropuntia.\n",
      "REFERENCE   1  (bases 1 to 1197)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1197)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1197\n",
      "                     /organism=\"Cylindropuntia tunicata\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:766221\"\n",
      "     gene            <1..>1197\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1094..>1197\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gtgatatacg aaacagtaag agcccatagt atgaagtatg aactaataac tatagaacta\n",
      "       61 ataaccaact catcgcatca cattatctgg atccaaagaa gcagtcaaga taggatattt\n",
      "      121 tggtcctatc attgcagcaa ctgaattttt tttttcataa acaagaaatc gaatgagttg\n",
      "      181 tcaagcaaaa gaaaaaaaaa aaaagaaaaa tatacnttaa aggaggggga tgcggataaa\n",
      "      241 tggaaaggcg aaagaaagaa aaaaatgaat ctaaatgata tacgattcca ctatgtaagg\n",
      "      301 tctttgaatc atatcataaa agacaatgta ataaagcatg aatacagatt cacacataat\n",
      "      361 tatctgatat gaatctattc atagaaaaaa gaaaaaagta agagcctccg gccaataaag\n",
      "      421 actaagaggg gttggctcaa aaacaaagtt cattaagagc tcccattgta gaattcagac\n",
      "      481 ctaatcatta atcaagaagc gatgggaacg atgtaatcca tgaatacaga agattcaatt\n",
      "      541 gaaaaaagaa tcctaatgat tcattgggga ggatggcgga acgaaccaga gaccaattca\n",
      "      601 tctattctga aaagtgataa actaatccta taaaactaaa atagatattg aaagagtaaa\n",
      "      661 tattcgcccg cgaaaattcc ttttttatta aattgctcat attttatttt agcaatgcaa\n",
      "      721 tctaataaaa tatatctata caaaaaaaca tagacaaact atatatataa tatttcaaat\n",
      "      781 tcccttatat atccaaatat aaaaatatct aataaattag atgaatatca aagaatctat\n",
      "      841 tgatttagtg tattattaaa tgtatatctt aattcaatat tattattcta ttcattttta\n",
      "      901 ttcattttca aatttataat atattaatct atatattaat ttagaattct attctaattc\n",
      "      961 gaattcaatt tttaaatatt cattcatatt caattaaaat tgaaattttt tcattcgcga\n",
      "     1021 ggagccggat gagaagaaac tctcatgtcc ggttctgtag tagagatgga attaagaaaa\n",
      "     1081 aaccatcaac tataacccca aaagaaccag attctgtaaa caacatagag gaagaatgaa\n",
      "     1141 gggaatatct tatcggggga atcgtatttg tttcggaaaa tatgctctca ggcacga\n",
      "//\n",
      "\n",
      "LOCUS       HM041481                1200 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Opuntia palmadora ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041481\n",
      "VERSION     HM041481.1  GI:330887240\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia palmadora\n",
      "  ORGANISM  Opuntia palmadora\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1200)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1200)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1200\n",
      "                     /organism=\"Opuntia palmadora\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001118\"\n",
      "     gene            <1..>1200\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1098..>1200\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 tgatatacga aaagtaagag cccatagtat gaagtatgaa ctaataacta tagaactaat\n",
      "       61 aaccaactca tcgcatcaca ttatctggat ccaaagaagc agtcaagata ggatattttg\n",
      "      121 gtcctatcat tgcagcaact gaattttttt ttcataaaca agaaatcaaa tgagttgtca\n",
      "      181 agcaaaagaa aaaaaaaaga aaaatatacn ttaaaggagg gggatgcgga taaatggaaa\n",
      "      241 ggcgaaagaa agaaaaaaat gaatctaaat gatatacgat tccactatgt aaggtctttg\n",
      "      301 aatcatatca taaaagacaa tgtaataaag catgaataca gattcacaca taattatctg\n",
      "      361 atatgaatct attcatagaa aaaagaaaaa agtaagagcc tccgggccaa taaagactaa\n",
      "      421 gagggttggg ctcaagaaca aagttcatta agagctccat tgtagaattc agacctaatc\n",
      "      481 attaatcaag aagcgatggg aacgatgtaa tccatgaata cagaagattc aattgaaaaa\n",
      "      541 gaatcctaat gattcattgg gaaggatggc ggaacgaacc agagaccaat tcatctattc\n",
      "      601 tgaaaagtga taaactaatc ctataaaact aaaatagata ttgaaagagt aaatattcgc\n",
      "      661 ccgcgaaaat tcctttttta ttaaattgct cacattttat tttagcaatg caatctaata\n",
      "      721 aaatatatct atacaaaaaa atatagacaa actatatata taatatattt caaatttcct\n",
      "      781 tatatatcct aatataaaaa tatctaataa attagatgaa tatcaaagaa tctattgatt\n",
      "      841 tagtgtatta ttaaatgtat atcttaattc aatattatta ttctattcat ttttattatt\n",
      "      901 catttttatt cattttcaaa tttagaatat attaatctat atattaattt agaattctat\n",
      "      961 tctaattcga attcaatttt taaatattca tattcaatta aaattgaaat tttttcattc\n",
      "     1021 gcgaggagcc ggatgagaag aaactctcac gtccggttct gtagtagagg tggaattaag\n",
      "     1081 aaaaaaccat caactataac cccaaaagaa ccagattctg taaacaacat agaggaagaa\n",
      "     1141 tgaagggaat atcttatcgg gggaatcgta tttgtttcgg aagatatgct ctcagcacga\n",
      "//\n",
      "\n",
      "LOCUS       HM041480                1153 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Opuntia microdasys ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041480\n",
      "VERSION     HM041480.1  GI:330887239\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia microdasys\n",
      "  ORGANISM  Opuntia microdasys\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1153)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1153)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1153\n",
      "                     /organism=\"Opuntia microdasys\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:169217\"\n",
      "     gene            <1..>1153\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1079..>1153\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gcccatagta tgaagtatga actaataact atagaactaa taaccaactc atcgcatcac\n",
      "       61 attatctgga tccaaagaag cagtcaagat aggatatttt ggtcctatca ttgcagcaac\n",
      "      121 tgaatttttt ttttcataaa caagaaatca aatgagttgt caagcaaaag aaaaaaaaaa\n",
      "      181 aaaaaaatat actttaaggg ggggggatgg ggataaaggg aaaggggaaa aaaaaaaaaa\n",
      "      241 aatgaatcta aatgatatac aattccacta tgaaaggtct ttgaatcata tcaaaaaaaa\n",
      "      301 caatgtaata aagcaggaat acagattccc acataattat ctgatatgaa tcttttcata\n",
      "      361 aaaaaaaaaa aaaagtaaga gcctccggcc aataaagact aagagggttg gctcaagaac\n",
      "      421 aaagttcatt aagggctcca ttgtagaatt cagacctaat cattaatcaa gaggcgatgg\n",
      "      481 gaacgatgta atccatgaat acagaagatt caattgaaaa agaatcctaa tgattcattg\n",
      "      541 ggaaggatgg cggaacgaac cagagaccaa ttcatctatt ctgaaaagtg aaaaactaat\n",
      "      601 cctataaaac taaaatagat attgaaagag taaatattcg cccgcgaaaa ttcctttttt\n",
      "      661 attaaattgc tcacatttta ttttagcaat gcaatctaat aaaatatatc tatacaaaaa\n",
      "      721 aatatagaca aactatatat ataatatatt tcaaatttcc ttatatatcc taatataaaa\n",
      "      781 atatctaata aattagatga atatcaaaga atctattgat ttagtgtatt attaaatgta\n",
      "      841 tatcttaatt caatattatt attctattca tttttattat tcatttttat tcattttcaa\n",
      "      901 atttagaata tattaatcta tatattaatt tataattcta ttctaattcg aattcaattt\n",
      "      961 ttaaatattc atattcaatt aaaattgaaa ttttttcatt cgcgaggagc cggatgagaa\n",
      "     1021 gaaactctca cgtccggttc tgtagtagag gtggaattaa gaaaaaacca tcaactataa\n",
      "     1081 ccccaaaaga accagattct gtaaacaaca tagaggaaga atgaagggaa tatcttatcg\n",
      "     1141 ggggatatcg tat\n",
      "//\n",
      "\n",
      "LOCUS       HM041479                1197 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Opuntia megasperma ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041479\n",
      "VERSION     HM041479.1  GI:330887238\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia megasperma\n",
      "  ORGANISM  Opuntia megasperma\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1197)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1197)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1197\n",
      "                     /organism=\"Opuntia megasperma\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001117\"\n",
      "     gene            <1..>1197\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1098..>1197\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gatatacgaa aagtaagagc ccatagtatg aagtatgaac taataactat agaactaata\n",
      "       61 accaactcat cgcatcacat tatccggatc caaagaagca gtcaagatag gatattttgg\n",
      "      121 tcctatcatt gcagcaactg aatttttttt tcataaacaa gaaatcaaat gagttgtcaa\n",
      "      181 gcaaaagaaa aaaaaaaaag aaaaatatac tttaaaggag ggggatgcgg ataaatggaa\n",
      "      241 aggcgaaaga aagaaaaaaa tgaatctaaa tgatatacga ttccnctatg taaggtcttt\n",
      "      301 gaatcatatc ataaaagaca atgtaataaa gcatgaatac agattcacac ataattatct\n",
      "      361 gatatgaatc tattcataga aaaaagaaaa aagtaagagc ctccgggcca ataaagacta\n",
      "      421 agagggttgg ctcaagaaca aagttcatta agagctccat tgtagaattc agacctaatc\n",
      "      481 attaatcaag aagcgatggg aacgatgtaa tccatgaata cagaagattc aattgaaaaa\n",
      "      541 gaatcctaat gattcattgg gaaggatggc ggaacgaacc agagaccaat tcatctattc\n",
      "      601 tgaaaagtga taaactaatc ctataaaact aaaatagata ttgaaagagt aaatattcgc\n",
      "      661 ccgcgaaaat tcctttttta ttaaattgct cacattttat tttagcaatg caatctaata\n",
      "      721 aaatatatct atacaaaaaa atatagacaa actatatata taatatattt caaatttcct\n",
      "      781 tatatatcct aatataaaaa tatctaataa attagatgaa tatcaaagaa tctattgatt\n",
      "      841 tagtgtatta ttaaatgtat atcttaattc aatattttta ttctattcat ttttattatt\n",
      "      901 catttttatt cattttcaaa tttagaatat attaatctat atattaattt agaattctat\n",
      "      961 tctaattcga attcaatttt taaatattca tattcaatta aaattgaaat tttttcattc\n",
      "     1021 gcgaggagcc ggatgagaag aaactctcac gtccggttct gtagtagagg tggaattaag\n",
      "     1081 aaaaaaccat caactataac cccaaaagaa ccagattctg taaacaacat agaggaagaa\n",
      "     1141 tgaagggaat atcttatcgg gggaatcgta tttgtttcgg aagatatgct ctcagca\n",
      "//\n",
      "\n",
      "LOCUS       HM041478                1187 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Opuntia macbridei ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041478\n",
      "VERSION     HM041478.1  GI:330887237\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia macbridei\n",
      "  ORGANISM  Opuntia macbridei\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1187)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1187)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1187\n",
      "                     /organism=\"Opuntia macbridei\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001116\"\n",
      "     gene            <1..>1187\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1090..>1187\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 aaaagtaaga gcccatagta tgaagtatga actaataact atagaactaa taaccaactc\n",
      "       61 atcgcatcac attatctgga tccaaagaag cagtcaagat aggatatttt ggtcctatca\n",
      "      121 ttgcagcaac tgaatttttt tttcataaac aagaaatcaa atgagttgtc aagcaaaaga\n",
      "      181 aaaaaaaaaa agaaaaatat acattaaagg agggggatgc ggataaatgg aaaggcgaaa\n",
      "      241 gaaagaaaaa aatgaatcta aatgatatac gattccacta tgtaaggtct ttgaatcata\n",
      "      301 tcataaaaga caatgtaata aagcatgaat acagattcac acataattat ctgatatgaa\n",
      "      361 tctattcata gaaaaaagaa aaaagtaaga gcctccggcc aataaagact aagagggttg\n",
      "      421 gctcaagaac aaagttcatt aagggctcca tttgtagaat tcagacctaa tcattaatca\n",
      "      481 agaagcgatg ggaacgatgt aattccatga atacagaaga ttcaattgaa aaagatccta\n",
      "      541 atgattcatt gggaaggatg gcggacgaac cagagaccaa ttcatctatt ctgaaaagtg\n",
      "      601 ataaactaat cctataaaac taaaatagat attgaaagag taaatattcg cccgcgaaaa\n",
      "      661 ttcctttttt attaaattgc tcacatttta ttttagcaat gcaatctaat aaaatatatc\n",
      "      721 tatacaaaaa aaatatagac aaactatata tataatatat ttcaaatttc cttatatatc\n",
      "      781 ctaatataaa aatatctaat aatttagatg aatatcaaag aatctattga tttagtgtat\n",
      "      841 tattaaatgt atatcttaat tcaatattat tattctattc atttttatta ttcattttta\n",
      "      901 ttcattttca aatttagaat atattaatct atatattaat ttagaattct attctaattc\n",
      "      961 gaattcaatt tttaaatatt catattcaat taaaattgaa attttttcat tcgcgaggag\n",
      "     1021 ccggatgaga agaaactctc acgtccggtt ctgtagtaga ggtggaatta agaaaaaacc\n",
      "     1081 atcaactata accccaaaag aaccagattc tgtaaacaac atagaggaag aatgaaggga\n",
      "     1141 atatcttatc gggggaatcg tatttgtttc ggaagatatg ctctcag\n",
      "//\n",
      "\n",
      "LOCUS       HM041477                1197 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Cylindropuntia leptocaulis ribosomal protein L16-like (rpl16) gene,\n",
      "            partial sequence; chloroplast.\n",
      "ACCESSION   HM041477\n",
      "VERSION     HM041477.1  GI:330887236\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Cylindropuntia leptocaulis\n",
      "  ORGANISM  Cylindropuntia leptocaulis\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Cylindropuntia.\n",
      "REFERENCE   1  (bases 1 to 1197)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1197)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1197\n",
      "                     /organism=\"Cylindropuntia leptocaulis\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:866983\"\n",
      "     gene            <1..>1197\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1096..>1197\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 ttgtgngnct cctgaagagt aggagcccct agtatgaagt atgaactaat aactatagaa\n",
      "       61 ctaataacca actcatcgca tcacattatc cggatccaaa aaagcagtca agataggata\n",
      "      121 ttttggtcct atcattgcag caactgaatt ttttttttca taaacaagaa atcgaatgag\n",
      "      181 ttgtcaagca aaagaaaaaa aaagaaaaat atactttaaa ggagggggat gcggataaat\n",
      "      241 ggaaaggcga aagaaagaaa aaaatgaatc taaatgatat aggattcccc tatgtaaggt\n",
      "      301 ctttgaatca tatcataaaa gacaatgtaa taaagcatga atacagattc ccacataatt\n",
      "      361 atctgatatg aatctattcc tagaaaaaag aaaaaagtaa gagcctccgg ccaataaaga\n",
      "      421 ctaagagggt tggctcaaga acaaagttca ttaaaagctc ccttgtagaa ttcagaccta\n",
      "      481 atcnttaatc aagaagcgat gggaacgatg taatccctga atacagaaga ttcaattgaa\n",
      "      541 aaagaatcct aatgattcat tgggaaggat ggcggaacga accagagacc aattcatcta\n",
      "      601 ttctgaaaag tgataaacta atcctataaa actaaaatag atattgaaag agtaaatatt\n",
      "      661 cgcccgcgaa atttcctttt ttattaaatt gctcatattt ttttttagca atgcaatcta\n",
      "      721 ataaaatata tctctacaaa aaaacataga caaactatat atatatatat atataatatt\n",
      "      781 tcaaattccc ttatatatcc aaatataaaa atatctaata aattagatga atatcaaaga\n",
      "      841 atctattgat ttagtgtatt attaaatgta tatcttaatt caatattatt attctattca\n",
      "      901 tttttattca ttttcaaatt tataatatat taatctatat attaatatag aattctattc\n",
      "      961 taattcgaat tcaattttta aatattcata ttcaattaaa attgaaattt tttcattcgc\n",
      "     1021 gaggagccgg atgagaagaa actctcatgt ccggttctgt agtagagatg gaattaagaa\n",
      "     1081 aaaaccatca actataaccc caaaagaacc ggattctgta aacaacatag aggaagaatg\n",
      "     1141 aagggaatat cttgtcgggg gaatcgatnn gtncggaant natgntcgcn gcgcgcc\n",
      "//\n",
      "\n",
      "LOCUS       HM041476                1205 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Opuntia lasiacantha ribosomal protein L16-like (rpl16) gene,\n",
      "            partial sequence; chloroplast.\n",
      "ACCESSION   HM041476\n",
      "VERSION     HM041476.1  GI:330887235\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia lasiacantha\n",
      "  ORGANISM  Opuntia lasiacantha\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1205)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1205)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1205\n",
      "                     /organism=\"Opuntia lasiacantha\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:547104\"\n",
      "     gene            <1..>1205\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1103..>1205\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gggcccnnna ngangaaaag tagagcccat agtatgaagt atgaactaat aactatagaa\n",
      "       61 ctaataacca actcatcgca tcacattatc tggatccaaa gaagcagtca agataggata\n",
      "      121 ttttggtcct atcattgcag caactgaatt ttttttttca taaacaagaa atcaaatgag\n",
      "      181 ttgtcaagca aaagaaaaaa aaaaagaaaa atatccttta aaggaggggg atgcggataa\n",
      "      241 atggaaaggc gaaagaaaga aaaaaatgaa tctaaatgat atacgattcc cctatgtaag\n",
      "      301 gtctttgaat catatcataa aagacaatgt aataaagcat gaatacagat tcccccataa\n",
      "      361 ttatctgata tgaatctatt cctagaaaaa agaaaaaagt aagagcctcc ggccaataaa\n",
      "      421 gactaagagg gttggctcaa gaacaaagtt cattaagggc tccattgtag aattcagacc\n",
      "      481 taatcattaa tcaagaggcg atgggaacga tgtaatccat gaatacagaa gattcaattg\n",
      "      541 aaaaagaatc ctaatgattc attgggaagg atggcggaac gaaccagaga ccaattcatc\n",
      "      601 tattctgaaa agtgataaac taatcctata aaactaaaat agatattgaa agagtaaata\n",
      "      661 ttcgcccgcg aaaattcctt ttttattaaa ttgctcacat tttattttag caatgcaatc\n",
      "      721 taataaaatc tatctataca aaaaaatata gacaaactat atatataata tatttcaaat\n",
      "      781 ttccttatat atcctaatat aaaaatatct aataaattag atgaatatca aagaatctat\n",
      "      841 tgatttagtg tattattaaa tgtatatctt aattcaatat tattattcta ttcattttta\n",
      "      901 ttattcattt ttattcattt tcaaatttag aatatattaa tctatatatt aatttataat\n",
      "      961 tctattctaa ttcgaattca atttttaaat attcatattc aattaaaatt gaaatttttt\n",
      "     1021 cattcgcgag gagccggatg agaagaaact ctcacgtccg gttctgtagt agaggtggaa\n",
      "     1081 ttaagaaaaa accatcaact ataaccccaa aagaaccaga ttctgtaaac aacatagagg\n",
      "     1141 aagaatgaag ggaatatctt atcgagggaa tcgtatttgt ttcggaagat agtnctngcn\n",
      "     1201 nggtg\n",
      "//\n",
      "\n",
      "LOCUS       HM041474                1163 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Opuntia helleri ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041474\n",
      "VERSION     HM041474.1  GI:330887233\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia helleri\n",
      "  ORGANISM  Opuntia helleri\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1163)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1163)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1163\n",
      "                     /organism=\"Opuntia helleri\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001115\"\n",
      "     gene            <1..>1163\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1081..>1163\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gagcccatag tatgaagtat gaactaataa ctatagaact aataaccaac tcatcgcatc\n",
      "       61 acattatccg gatccaaaga agcagtcaag ataggatatt ttggtcctat cattgcagca\n",
      "      121 actgaatttt tttttcataa acaagaaatc aaatgagttg tcaagcaaaa gaaaaaaaaa\n",
      "      181 aaagaaaaat atacattaaa ggagggggat gcggataaat ggaaaggcga aagaaagaaa\n",
      "      241 aaaatgaatc taaatgatat acgattccnc tatgtaaggt ctttgaatca tatcataaaa\n",
      "      301 gacaatgtaa taaagcatga atacagattc acacataatt atctgatatg aatctattca\n",
      "      361 tagaaaaaag aaaaaagtaa gagcctccgg ccaataaaga ctaagagggt tggctcaaga\n",
      "      421 acaaagttca ttaagggctc cattgtagaa ttcagaccta atcattaatc aagaagcgat\n",
      "      481 gggaacgatg taatccatga atacagaaga ttcaattgaa aaagaatcct aatgattcat\n",
      "      541 tgggaaggat ggcggaacga accagagacc aattcatcta ttctgaaaag tgataaacta\n",
      "      601 atcctataaa actaaaatag atattgaaag agtaaatatt cgcccgcgaa aattcctttt\n",
      "      661 ttattaaatt gctcacattt tattttagca atgcaatcta ataaaatata tctatacaaa\n",
      "      721 aaaatataga caaactatat atataatata tttaaaattt ccttatatat cctaatataa\n",
      "      781 aaatatctaa taaattagat gaatatcaaa gaatctattg atttagtgta ttattaaatg\n",
      "      841 tatatcttaa ttcaatattt ttattctatt catttttatt attcattttt attcattttc\n",
      "      901 aaatttagaa tatattaatc tatatattaa tttagaattc tattctaatt cgaattcaat\n",
      "      961 ttttaaatat tcatattcaa ttaaaattga aattttttca ttcgcgagga gccggatgag\n",
      "     1021 aagaaactct cacgtccggt tctgtagtag aggtggaatt aagaaaaaac catcaactat\n",
      "     1081 aaccccaaaa gaaccagatt ctgtaaacaa catagaggaa gaatgaaggg aatatcttat\n",
      "     1141 cgggggaatc gtatttgttt cgg\n",
      "//\n",
      "\n",
      "LOCUS       HM041473                1203 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Opuntia excelsa ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041473\n",
      "VERSION     HM041473.1  GI:330887232\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia excelsa\n",
      "  ORGANISM  Opuntia excelsa\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1203)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1203)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1203\n",
      "                     /organism=\"Opuntia excelsa\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:867487\"\n",
      "     gene            <1..>1203\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1103..>1203\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 ccgnncnttg nnanacagaa nagtagagcc cnttntntga agtatgaact aatcactatt\n",
      "       61 gaactaatcc ccnactcatc gcatcacatt atctggatcc aaagaagcag tcaagatagg\n",
      "      121 atattttggt cctatcattg cagcaactga attttttttt tcctaaacaa gaaatcaaat\n",
      "      181 gagttgtcaa gcaaaagaaa aaaaagaaaa atatacatta aaggaggggg atgcggataa\n",
      "      241 atggaaaggc gaaagaaaga aaaaaatgaa tctaaatgat atacgattcc cctatgtaag\n",
      "      301 gtctttgaat catatcataa aagacaatgt aataaagcat gaatacagat tcccacataa\n",
      "      361 ttatctgata tgaatctatt catagaaaaa agaaaaaagt aagagcctcc ggccaataaa\n",
      "      421 gactaaaagg gttggctcaa gaacaaagtt cattaagggc tccattgtaa aattcagacc\n",
      "      481 taatcattaa tcaagaggcg atgggaacga tgtaatccat gaatacagaa gattcaattg\n",
      "      541 aaaaagaatc ctaatgattc attgggaagg atggcggaac gaaccagaga ccaattcatc\n",
      "      601 tattctgaaa agtgataaac taatcctata aaactaaaat agatattgaa agagtaaata\n",
      "      661 ttcgcccgcg aaaattcctt ttttattaaa ttgctcacat tttattttag caatgcaatc\n",
      "      721 taataaaatc tatctataca aaaaaatata gacaaactat atatataata tatttcaaat\n",
      "      781 ttccttatat atcctaatat aaaaatatct aataaattag atgaatatca aagaatctat\n",
      "      841 tgatttagtg tattattaaa tgtatatctt aattcaatat tattattcta ttcattttta\n",
      "      901 ttattcattt ttattcattt tcaaatttag aatatattaa tctatatatt aatttagaat\n",
      "      961 tctattctaa ttcgaattca atttttaaat attcatattc aattaaaatt gaaatttttt\n",
      "     1021 cattcgcgag gagccggatg agaagaaact ctcacgtccg gttctgtagt agaggtggaa\n",
      "     1081 ttaagaaaaa accatcaact ataaccccaa aagaaccaga ttctgtaaac aacatagagg\n",
      "     1141 aagaatgaag ggaatatctt atcgggggaa tcgtatngtg cnggctngtg cancgcgggc\n",
      "     1201 nng\n",
      "//\n",
      "\n",
      "LOCUS       HM041472                1182 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Opuntia echios ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041472\n",
      "VERSION     HM041472.1  GI:330887231\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia echios\n",
      "  ORGANISM  Opuntia echios\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1182)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1182)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1182\n",
      "                     /organism=\"Opuntia echios\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:412453\"\n",
      "     gene            <1..>1182\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1085..>1182\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gtaagagccc atagtatgaa gtatgaacta ataactatag aactaataac caactcatcg\n",
      "       61 catcacatta tccggatcca aagaagcagt caagatagga tattttggtc ctatcattgc\n",
      "      121 agcaactgaa tttttttttc ataaacaaga aatcaaatga gttgtcaagc aaaagaaaaa\n",
      "      181 aaaaaaaaaa aaatatacat taaaggaggg ggatgcggat aaatggaaag gcgaaagaaa\n",
      "      241 gaaaaaaatg aatctaaatg atatacgatt ccactatgta aggtctttga atcatatcat\n",
      "      301 aaaagacaat gtaataaagc atgaatacag attcacacat aattatctga tatgaatcta\n",
      "      361 ttcatagaaa aaagaaaaaa gtaagagcct ccggccaata aagactaaga ggttgggctc\n",
      "      421 aagaacaaag ttcattaagg gctccattgt agaattcaga cctaatcatt aatcaagaag\n",
      "      481 cgatgggaac gatgtaatcc atgaatacag aagattcaat tgaaaaagaa tcctaatgat\n",
      "      541 tcattgggaa ggatggcgga acgaaccaga gaccaattca tctattctga aaagtgataa\n",
      "      601 actaatccta taaaactaaa atagatattg aaagagtaaa tattcgcccg cgaaaattcc\n",
      "      661 ttttttatta aattgctcac attttatttt agcaatgcaa tctaataaaa tatatctata\n",
      "      721 caaaaaaata tagacaaact atatatataa tatatttcaa atttccttat atatcctaat\n",
      "      781 ataaaaatat ctaataaatt agatgaatat caaagaatct attgatttag tgtattatta\n",
      "      841 aatgtatatc ttaattcaat attattattc tattcatttt tattattcat ttttattcat\n",
      "      901 tttcaaattt agaatatatt aatctatata ttaatttaga attctattct aattcgaatt\n",
      "      961 caatttttaa atattcatat tcaattaaaa ttgaaatttt ttcattcgcg aggagccgga\n",
      "     1021 tgagaagaaa ctctcacgtc cggttctgta gtagaggtgg aattaagaaa aaaccatcaa\n",
      "     1081 ctataacccc aaaagaacca gattctgtaa acaacataga ggaagaatga agggaatatc\n",
      "     1141 ttatcggggg aatcgtattt gtttcggaag atggctacta ta\n",
      "//\n",
      "\n",
      "LOCUS       HM041469                1189 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Nopalea sp. THH-2011 ribosomal protein L16-like (rpl16) gene,\n",
      "            partial sequence; chloroplast.\n",
      "ACCESSION   HM041469\n",
      "VERSION     HM041469.1  GI:330887228\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia sp. THH-2011\n",
      "  ORGANISM  Opuntia sp. THH-2011\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1189)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1189)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1189\n",
      "                     /organism=\"Opuntia sp. THH-2011\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001114\"\n",
      "     gene            <1..>1189\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1096..>1189\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 atatacgaaa aagtagagcc catagtatga agtatgaact aataactata gaactaataa\n",
      "       61 ccaactcatc gcatcacatt atctggatcc aaagaagcag tcaagatagg atattttggt\n",
      "      121 cctatcattg cagcaactga attttttttt cataaacaag aaatcaaatg agttgtcaag\n",
      "      181 caaaagaaaa aaaaaaaaga aaaatatact ttaagggagg gggatgcgga taaatggaaa\n",
      "      241 ggcgaaagaa agaaaaaaat gaatctaaat gatatacgat tccactatgt aaggtctttg\n",
      "      301 aatcatatca taaaagacaa tgtaataaag catgaataca gattcacaca taattatctg\n",
      "      361 gtatgaatct attcatagaa aaaagaaaaa agtaagaccc tccggccaat aaagactaag\n",
      "      421 agggttggct caagaacaaa gttcattaag ggctccattg tagaattcag acctaatcat\n",
      "      481 taatcaagaa gcgatgggaa cgatgtaatc catgaataca gaagattcaa ttgaaaaaga\n",
      "      541 atcctaatga ttcattggga aggatggcgg aacgaaccag agaccaattc atctattctg\n",
      "      601 aaaagtgata aactaatcct ataaaactaa aatagatatt gaaagagtaa atattcgccc\n",
      "      661 gcgaaaattc cttttttatt aaattgctca cattttattt tagcaatgca atctaataaa\n",
      "      721 atatatctat acaaaaaaat atagacaaac tatatatata atatatttca aatttcctta\n",
      "      781 tatatcctaa tataaaaata tctaataaat tagatgaata tcaaagaatc tattgattta\n",
      "      841 gtgtattatt aaatgtatat cttaattcaa tattattatt ctattcattt ttattattca\n",
      "      901 tttttattca ttttcaaatt tagaatatat taatctatat attaatttag aattctattc\n",
      "      961 taattcgaat tcaattttta aatattcata ttcaattaaa attgaaattt tttcattcgc\n",
      "     1021 gaggagccgg atgagaagaa actctcacgt ccggttctgt agtagaggtg gaattaagaa\n",
      "     1081 aaaaccatca actataaccc caaaagaacc agattctgta aacaacatag aggaagaatg\n",
      "     1141 aagggaatat cttatcgggg gaatcgtatt tgtttcggaa gatatgctc\n",
      "//\n",
      "\n",
      "LOCUS       HM041468                1202 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Nopalea lutea ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041468\n",
      "VERSION     HM041468.1  GI:330887227\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia lutea\n",
      "  ORGANISM  Opuntia lutea\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1202)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1202)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1202\n",
      "                     /organism=\"Opuntia lutea\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001113\"\n",
      "     gene            <1..>1202\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1099..>1202\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gatatacgaa aaagtaagag cccatagtat gaagtatgaa ctaataacta tagaactaat\n",
      "       61 aaccaactca tcgcatcaca ttatctggat ccaaagaagc agtcaagata ggatattttg\n",
      "      121 gtcctatcat tgcagcaact gaattttttt ttcataaaca agaaatcaaa tgagttgtca\n",
      "      181 agcaaaagaa aaaaaaaaaa gaaaaatata ctttaaggga gggggatgcg gataaatgga\n",
      "      241 aaggcgaaag aaagaaaaaa atgaatctaa atgatatacg attcccccta tgtaaggtct\n",
      "      301 ttgaatcata tcataaaaga caatgtaata aagcatgaat acagattcac acataattat\n",
      "      361 ctgatatgaa tctattcata gaaaaaagaa aaaagtaaga ccctccggcc aataaagact\n",
      "      421 aagagggttg gctcaagaac aaagttcatt aagggctcca ttgtagaatt cagacctaat\n",
      "      481 cattaatcaa gaagcgatgg gaacgatgta atccatgaat acagaagatt caattgaaaa\n",
      "      541 agaatcctaa tgattcattg ggaaggatgg cggaacgaac cagagaccaa ttcatctatt\n",
      "      601 ctgaaaagtg ataaactaat cctataaaac taaaatagat attgaaagag taaatattcg\n",
      "      661 cccgcgaaaa ttcctttttt attaaattgc tcacatttta ttttagcaat gcaatctaat\n",
      "      721 aaaatatatc tatacaaaaa aatatagaca aactatatat ataatatatt tcaaatttcc\n",
      "      781 ttatatatcc taatataaaa atatctaata aattagatga atatcaaaga atctattgat\n",
      "      841 ttagtgtatt attaaatgta tatcttaatt caatattatt attctattca tttttattat\n",
      "      901 tcatttttat tcattttcaa atttagaata tattaatcta tatattaatt tagaattcta\n",
      "      961 ttctaattcg aattcaattt ttaaatattc atattcaatt aaaattgaaa ttttttcatt\n",
      "     1021 cgcgaggagc cggatgagaa gaaactctca cgtccggttc tgtagtagag gtggaattaa\n",
      "     1081 gaaaaaacca tcaactataa ccccaaaaga accagattct gtaaacaaca tagaggaaga\n",
      "     1141 atgaagggaa tatcttatcg ggggaatcgt atttgtttcg gaagatatgc tctcaggcac\n",
      "     1201 ga\n",
      "//\n",
      "\n",
      "LOCUS       HM041467                1199 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Nopalea karwinskiana ribosomal protein L16-like (rpl16) gene,\n",
      "            partial sequence; chloroplast.\n",
      "ACCESSION   HM041467\n",
      "VERSION     HM041467.1  GI:330887226\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia karwinskiana\n",
      "  ORGANISM  Opuntia karwinskiana\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1199)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1199)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1199\n",
      "                     /organism=\"Opuntia karwinskiana\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001112\"\n",
      "     gene            <1..>1199\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1098..>1199\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gtgatatcga aaaagtagag cccatagtat gaagtatgaa ctaataacta tagaactaat\n",
      "       61 aaccaactca tcgcatcaca ttatctggat ccaaagaagc agtcaagata ggatattttg\n",
      "      121 gtcctatcat tgcagcaact gaattttttt ttcataaaca agaaatcaaa tgagttgtca\n",
      "      181 agcaaaagaa aaaaaaaaaa gaaaaattta ctttaaggga gggggatgcg gataaatgga\n",
      "      241 aaggcgaaag aaagaaaaaa atgaatctaa atgatatacg attcccctat gtagggtctt\n",
      "      301 tgaatcatat cataaaaaac aatgtaataa agcatgaata cagattcccc cataattatc\n",
      "      361 tggtatgaat cttttcatag aaaaaaaaaa aaagtaagag cctccggcca ataaaaacta\n",
      "      421 aaagggttgg ctcaagaaca aagttcatta agggctccat tgtagaattc agacctaatc\n",
      "      481 nttaatcaag aagcgatggg aacgatgtaa tccatgaata cagaagattc aattgaaaaa\n",
      "      541 gaatcctaat gattcattgg gaaggatggc ggaacgaacc agagaccaat tcatctattc\n",
      "      601 tgaaaagtga taaactaatc ctataaaact aaaatagata ttgaaagagt aaatattcgc\n",
      "      661 ccgcgaaaat tcctttttta ttaaattgct cacattttat tttagcaatg caatctaata\n",
      "      721 aaatatatct atacaaaaaa atatagacaa actatatata taatatattt caaatttcct\n",
      "      781 tatatatcct aatataaaaa tatctaataa attagatgaa tatcaaagaa tctattgatt\n",
      "      841 tagtgtatta ttaaatgtat atcttaattc aatattatta ttctattcat ttttattatt\n",
      "      901 catttttatt cattttcaaa tttagaatat attaatctat atattaattt agaattctat\n",
      "      961 tctaattcga attcaatttt taaatattca tattcaatta aaattgaaat tttttcattc\n",
      "     1021 gcgaggagcc ggatgagaag aaactctcac gtccggttct gtagtagagg tggaattaag\n",
      "     1081 aaaaaaccat caactataac cccaaaagaa ccagattctg taaacaacat agaggaagaa\n",
      "     1141 tgaagggaat atcttatgcg ggggaatcgt attgtttcgg aagatatgct ctgcggccc\n",
      "//\n",
      "\n",
      "LOCUS       HM041466                1205 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Nopalea gaumeri ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041466\n",
      "VERSION     HM041466.1  GI:330887225\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Nopalea gaumeri\n",
      "  ORGANISM  Nopalea gaumeri\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1205)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1205)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1205\n",
      "                     /organism=\"Nopalea gaumeri\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001111\"\n",
      "     gene            <1..>1205\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1103..>1205\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gctgtgatat acgaaanagt aagagcccat agtatgaagt atgaactaat aactatagaa\n",
      "       61 ctaataacca actcatcgca tcacattatc tggatccaaa gaagcagtca agataggata\n",
      "      121 ttttggtcct atcattgcag caactgaatt tttttttcat aaacaagaaa tcaaatgagt\n",
      "      181 tgtcaagcaa aagaaaaaaa aaaaaaaaaa tatacattaa aggaggggga tgcggataaa\n",
      "      241 tggaaaggcg aaagaaagaa aaaaatgaat ctaaatgata tacgattcca ctatgtaagg\n",
      "      301 tctttgaatc atatcataaa agacaatgta ataaagcatg aatacagatt cacacataat\n",
      "      361 tatctgaata tgaatctatt catagaaaaa agaaaaaagt aagaccctcc ggccaataaa\n",
      "      421 gactaaaggg gttggctcaa gaacaaagtt cattaagggc tccattgtag aattcagacc\n",
      "      481 taatcattaa tcaagaagcg atgggaacga tgtaatccat gaatacagaa gattcaattg\n",
      "      541 aaaaagaatc ctaatgattc attgggaagg atggcggaac gaaccagaga ccaattcatc\n",
      "      601 tattctgaaa agtgataaac taatcctata aaactaaaat agatattgaa agagtaaata\n",
      "      661 ttcgcccgcg aaaattcctt ttttattaaa ttgctcacat tttattttag caatgcaatc\n",
      "      721 taataaaata tatctataca aaaaaatata gacaaactat atatataata tatttcaaat\n",
      "      781 ttccttatat atcctaatat aaaaatatct aataaattag atgaatatca aagaatctat\n",
      "      841 tgatttagtg tattattaaa tgtatatctt aattcaatat tattattcta ttcattttta\n",
      "      901 ttattcattt ttattcattt tcaaatttag aatatattaa tctatatatt aatttagaat\n",
      "      961 tctattctaa ttcgaattca atttttaaat attcatattc aattaaaatt gaaatttttt\n",
      "     1021 cattcgcgag gagccggatg agaagaaact ctcacgtccg gttctgtagt agaggtggaa\n",
      "     1081 ttaagaaaaa accatcaact ataaccccaa aagaaccaga ttctgtaaac aacatagagg\n",
      "     1141 aagaatgaag ggaatatctt atcgggggaa tcgtatttgt ttcggaagat atgctctcag\n",
      "     1201 cacga\n",
      "//\n",
      "\n",
      "LOCUS       HM041465                1190 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Nopalea dejecta ribosomal protein L16-like (rpl16) gene, partial\n",
      "            sequence; chloroplast.\n",
      "ACCESSION   HM041465\n",
      "VERSION     HM041465.1  GI:330887224\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia dejecta\n",
      "  ORGANISM  Opuntia dejecta\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1190)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1190)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1190\n",
      "                     /organism=\"Opuntia dejecta\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:1001110\"\n",
      "     gene            <1..>1190\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1096..>1190\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 tgatatacga aanagtaaga gcccatagta tgaagtatga actaataact atagaactaa\n",
      "       61 taaccaactc atcgcatcac attatctgga tccaaagaag cagtcaagat aggatatttt\n",
      "      121 ggtcctatca ttgcagcaac tgaatttttt tttcataaac aagaaatcaa atgagttgtc\n",
      "      181 aagcaaaaga aaaaaaaaaa aaaaaatata ctttaangga gggggatgcg gataaatgga\n",
      "      241 aaggcgaaag aaagaaaaaa atgaatctaa atgatatacg attccactat gtaaggtctt\n",
      "      301 tgaatcatat cataaaagac aatgtaataa agcatgaata cagattcaca cataattatc\n",
      "      361 tgtatgatct attcatagaa aaaagaaaaa agtaagagcc tccggccaat aaagactaag\n",
      "      421 agggttggct caagaacaaa gttcattaag ggctccattg tagaattcag acctaatcat\n",
      "      481 taatcaagaa gcgatgggaa cgatgtaatc catgaataca gaagattcaa ttgaaaaaga\n",
      "      541 atcctaatga ttcattggga aggatggcgg aacgaaccag agaccaattc atctattctg\n",
      "      601 aaaagtgata aactaatcct ataaaactaa aatagatatt gaaagagtaa atattcgccc\n",
      "      661 gcgaaaattc cttttttatt aaattgctca cattttattt tagcaatgca atctaataaa\n",
      "      721 atatatctat acaaaaaaat atagacaaac tatatatata atatatttca aatttcctta\n",
      "      781 tatatcctaa tataaaaata tctaataaat tagatgaata tcaaagaatc tattgattta\n",
      "      841 gtgtattatt aaatgtatat cttaattcaa tattattatt ctattcattt ttattattca\n",
      "      901 tttttattca ttttcaaatt tagaatatat taatctatat attaatttag aattctattc\n",
      "      961 taattcgaat tcaattttta aatattcata ttcaattaaa attgaaattt tttcattcgc\n",
      "     1021 gaggagccgg atgagaagaa actctcacgt ccggttctgt agtagaggtg gaattaagaa\n",
      "     1081 aaaaccatca actataaccc caaaagaacc agattctgta aacaacatag aggaagaatg\n",
      "     1141 aagggaatat cttatcgggg gaatcgtatt tgtttcggaa gatatgctct\n",
      "//\n",
      "\n",
      "LOCUS       HM041464                1184 bp    DNA     linear   PLN 03-MAY-2011\n",
      "DEFINITION  Nopalea cochenillifera ribosomal protein L16-like (rpl16) gene,\n",
      "            partial sequence; chloroplast.\n",
      "ACCESSION   HM041464\n",
      "VERSION     HM041464.1  GI:330887223\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia cochenillifera\n",
      "  ORGANISM  Opuntia cochenillifera\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 1184)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Hernandez,H.M., De-Nova,J.A., Puente,R.,\n",
      "            Eguiarte,L.E. and Magallon,S.\n",
      "  TITLE     Phylogenetic relationships and evolution of growth form in\n",
      "            Cactaceae (Caryophyllales, Eudicotyledoneae)\n",
      "  JOURNAL   Am. J. Bot. 98 (1), 44-61 (2011)\n",
      "   PUBMED   21613084\n",
      "REFERENCE   2  (bases 1 to 1184)\n",
      "  AUTHORS   Hernandez-Hernandez,T., Magallon,S.A., Hernandez,H.M., De-Nova,A.,\n",
      "            Puente,R. and Eguiarte,L.E.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (17-MAR-2010) Departamento de Botanica, Instituto de\n",
      "            Biologia, Universidad Nacional Autonoma de Mexico, 3er Circuito de\n",
      "            Ciudad Universitaria, Ciudad Universitaria, Coyoacan, Distrito\n",
      "            Federal C.P. 04510, Mexico\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..1184\n",
      "                     /organism=\"Opuntia cochenillifera\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:338184\"\n",
      "     gene            <1..>1184\n",
      "                     /gene=\"rpl16\"\n",
      "     misc_feature    <1102..>1184\n",
      "                     /gene=\"rpl16\"\n",
      "                     /note=\"similar to ribosomal protein L16\"\n",
      "ORIGIN      \n",
      "        1 gctgtgatat acgaaaaagt aagagcccat agtatgaagt atgaactaac aactatagaa\n",
      "       61 ctaataacca actcatcgca tcacattatc tggatccaaa gaagcagtca agataggata\n",
      "      121 ttttggtcct atcattgcag caactgaatt tttttttcat aaacaagaaa tcaaatgagt\n",
      "      181 tgtcaagcaa aagaaaaaaa aaaaaaaaaa tatactttaa aggaggggga tgcggataaa\n",
      "      241 tggaaaggcg aaagaaagaa aaaaatgaat ctaaatgata tacgattcca ctatgtaagg\n",
      "      301 tctttgaatc atatcataaa agacaatgta ataaagcatg aatacagatt cccacataat\n",
      "      361 tatctgatat gaatctattc atagaaaaaa gaaaaaagta agagcctccg gccaataaag\n",
      "      421 actaagaggg ttggctcaag aacaaagttc attaagggct ccattgtaga attcagacct\n",
      "      481 aatcattaat caagaagcga tgggaacgat gtaatccatg aatacagaag attcaattga\n",
      "      541 aaaagaatcc taatgattca ttgggaagga tggcggaacg aaccagagac caattcatct\n",
      "      601 attctgaaaa gtgataaact aatcctataa aactaaaata gatattgaaa gagtaaatat\n",
      "      661 tcgcccgcga aaattccttt tttattaaat tgctcacatt ttattttagc aatgcaatct\n",
      "      721 aataaaatat atctatacaa aaaaatatag acaaactata tatataatat atttcaaatt\n",
      "      781 tccttatata tcctaatata aaaatatcta ataaattaga tgaatatcaa agaatctatt\n",
      "      841 gatttagtgt attattaaat gtatatctta attcaatatt attattctat tcatttttat\n",
      "      901 tattcatttt tattcatttt caaatttaga atatattaat ctatatatta atttagaatt\n",
      "      961 ctattctaat tcgaattcaa tttttaaata ttcatattca attaaaattg aaattttttc\n",
      "     1021 attcgcgagg agccggatga gaagaaactc tcacgtccgg ttctgtagta gaggtggaat\n",
      "     1081 taagaaaaaa ccatcaacta taaccccaaa agaaccagat tctgtaaaca acatagagga\n",
      "     1141 agaatgaagg gaatatctta tcgggggaat cgtatttgtt tcgg\n",
      "//\n",
      "\n",
      "LOCUS       AY851612                 892 bp    DNA     linear   PLN 10-APR-2007\n",
      "DEFINITION  Opuntia subulata rpl16 gene, intron; chloroplast.\n",
      "ACCESSION   AY851612\n",
      "VERSION     AY851612.1  GI:57240072\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Austrocylindropuntia subulata\n",
      "  ORGANISM  Austrocylindropuntia subulata\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Austrocylindropuntia.\n",
      "REFERENCE   1  (bases 1 to 892)\n",
      "  AUTHORS   Butterworth,C.A. and Wallace,R.S.\n",
      "  TITLE     Molecular Phylogenetics of the Leafy Cactus Genus Pereskia\n",
      "            (Cactaceae)\n",
      "  JOURNAL   Syst. Bot. 30 (4), 800-808 (2005)\n",
      "REFERENCE   2  (bases 1 to 892)\n",
      "  AUTHORS   Butterworth,C.A. and Wallace,R.S.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (10-DEC-2004) Desert Botanical Garden, 1201 North Galvin\n",
      "            Parkway, Phoenix, AZ 85008, USA\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..892\n",
      "                     /organism=\"Austrocylindropuntia subulata\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:106982\"\n",
      "     gene            <1..>892\n",
      "                     /gene=\"rpl16\"\n",
      "     intron          <1..>892\n",
      "                     /gene=\"rpl16\"\n",
      "ORIGIN      \n",
      "        1 cattaaagaa gggggatgcg gataaatgga aaggcgaaag aaagaaaaaa atgaatctaa\n",
      "       61 atgatatacg attccactat gtaaggtctt tgaatcatat cataaaagac aatgtaataa\n",
      "      121 agcatgaata cagattcaca cataattatc tgatatgaat ctattcatag aaaaaagaaa\n",
      "      181 aaagtaagag cctccggcca ataaagacta agagggttgg ctcaagaaca aagttcatta\n",
      "      241 agagctccat tgtagaattc agacctaatc attaatcaag aagcgatggg aacgatgtaa\n",
      "      301 tccatgaata cagaagattc aattgaaaaa gatcctaatg atcattggga aggatggcgg\n",
      "      361 aacgaaccag agaccaattc atctattctg aaaagtgata aactaatcct ataaaactaa\n",
      "      421 aatagatatt gaaagagtaa atattcgccc gcgaaaattc cttttttatt aaattgctca\n",
      "      481 tattttattt tagcaatgca atctaataaa atatatctat acaaaaaaat atagacaaac\n",
      "      541 tatatatata taatatattt caaatttcct tatataccca aatataaaaa tatctaataa\n",
      "      601 attagatgaa tatcaaagaa tctattgatt tagtgtatta ttaaatgtat atcttaattc\n",
      "      661 aatattatta ttctattcat ttttattcat tttcaaattt ataatatatt aatctatata\n",
      "      721 ttaatttata attctattct aattcgaatt caatttttaa atattcatat tcaattaaaa\n",
      "      781 ttgaaatttt ttcattcgcg aggagccgga tgagaagaaa ctctcatgtc cggttctgta\n",
      "      841 gtagagatgg aattaagaaa aaaccatcaa ctataacccc aagagaacca ga\n",
      "//\n",
      "\n",
      "LOCUS       AY851611                 881 bp    DNA     linear   PLN 10-APR-2007\n",
      "DEFINITION  Opuntia polyacantha rpl16 gene, intron; chloroplast.\n",
      "ACCESSION   AY851611\n",
      "VERSION     AY851611.1  GI:57240071\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Opuntia polyacantha\n",
      "  ORGANISM  Opuntia polyacantha\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Opuntia.\n",
      "REFERENCE   1  (bases 1 to 881)\n",
      "  AUTHORS   Butterworth,C.A. and Wallace,R.S.\n",
      "  TITLE     Molecular Phylogenetics of the Leafy Cactus Genus Pereskia\n",
      "            (Cactaceae)\n",
      "  JOURNAL   Syst. Bot. 30 (4), 800-808 (2005)\n",
      "REFERENCE   2  (bases 1 to 881)\n",
      "  AUTHORS   Butterworth,C.A. and Wallace,R.S.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (10-DEC-2004) Desert Botanical Garden, 1201 North Galvin\n",
      "            Parkway, Phoenix, AZ 85008, USA\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..881\n",
      "                     /organism=\"Opuntia polyacantha\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:307728\"\n",
      "     gene            <1..>881\n",
      "                     /gene=\"rpl16\"\n",
      "     intron          <1..>881\n",
      "                     /gene=\"rpl16\"\n",
      "ORIGIN      \n",
      "        1 cattaaagga gggggatgcg gataaatgga aaggcgaaag aaagaaaaaa atgaatctaa\n",
      "       61 atgatatacg attccactat gtaaggtctt tgaatcatat cataaaagac aatgtaataa\n",
      "      121 agcatgaata cagattcaca cataattatc tgatatgaat ctattcatag aaaaaagaaa\n",
      "      181 aaagtaagag cctccggcca ataaagacta agagggttgg ctcaagaaca aagttcatta\n",
      "      241 agggctccat tgtagaattc agacctaatc attaatcaag aagcgatggg aacgatgtaa\n",
      "      301 tccatgaata cagaagattc aattgaaaaa gatcctaatg atcattggga aggatggcgg\n",
      "      361 aacgaaccag agaccaattc atctattctg aaaagtgata aactaatcct ataaaactaa\n",
      "      421 aatagatatt gaaagagtaa atattcgccc gcgaaaattc cttttttatt aaattgctca\n",
      "      481 cattttattt tagcaatgca atctaataaa atatatctat acaaaaaaat atagacaaac\n",
      "      541 tctatatata atatatttca aatttcctta tatatcctaa tataaaaata tctaataaat\n",
      "      601 tagatgaata tcaaagaatc tattgattta gtgtattatt aaatgtatat cttaattcaa\n",
      "      661 tattattatt ctattcattt tcaaatttag aatatattaa tctatatatt aatttagaat\n",
      "      721 tctattctaa ttcgaattca atttttaaat attcatattc aattaaaatt gaaatttttt\n",
      "      781 cattcgcgag gagccggatg agaagaaact ctcacgtccg gttactgtag tagaggtgga\n",
      "      841 attaagaaaa aaccatcaac tataacccca aaagaaccag a\n",
      "//\n",
      "\n",
      "LOCUS       AF191661                 895 bp    DNA     linear   PLN 07-NOV-1999\n",
      "DEFINITION  Opuntia kuehnrichiana rpl16 gene; chloroplast gene for chloroplast\n",
      "            product, partial intron sequence.\n",
      "ACCESSION   AF191661\n",
      "VERSION     AF191661.1  GI:6273287\n",
      "KEYWORDS    .\n",
      "SOURCE      chloroplast Cumulopuntia sphaerica\n",
      "  ORGANISM  Cumulopuntia sphaerica\n",
      "            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;\n",
      "            Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;\n",
      "            Pentapetalae; Caryophyllales; Cactineae; Cactaceae; Opuntioideae;\n",
      "            Cumulopuntia.\n",
      "REFERENCE   1  (bases 1 to 895)\n",
      "  AUTHORS   Dickie,S.L. and Wallace,R.S.\n",
      "  TITLE     Phylogeny of the subfamily Opuntioideae (Cactaceae)\n",
      "  JOURNAL   Unpublished\n",
      "REFERENCE   2  (bases 1 to 895)\n",
      "  AUTHORS   Dickie,S.L. and Wallace,R.S.\n",
      "  TITLE     Direct Submission\n",
      "  JOURNAL   Submitted (28-SEP-1999) Botany, Iowa State University, 353 Bessey\n",
      "            Hall, Ames, IA 50011-1020, USA\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..895\n",
      "                     /organism=\"Cumulopuntia sphaerica\"\n",
      "                     /organelle=\"plastid:chloroplast\"\n",
      "                     /mol_type=\"genomic DNA\"\n",
      "                     /db_xref=\"taxon:106979\"\n",
      "                     /note=\"subfamily Opuntioideae; synonym: Cumulopuntia\n",
      "                     kuenrichiana\"\n",
      "     gene            <1..>895\n",
      "                     /gene=\"rpl16\"\n",
      "     intron          <1..>895\n",
      "                     /gene=\"rpl16\"\n",
      "ORIGIN      \n",
      "        1 tatacattaa agaaggggga tgcggataaa tggaaaggcg aaagaaagaa aaaaatgaat\n",
      "       61 ctaaatgata tacgattcca ctatgtaagg tctttgaatc atatcataaa agacaatgta\n",
      "      121 ataaagcatg aatacagatt cacacataat tatctgatat gaatctattc atagaaaaaa\n",
      "      181 gaaaaaagta agagcctccg gccaataaag actaagaggg ttggctcaag aacaaagttc\n",
      "      241 attaagagct ccattgtaga attcagacct aatcattaat caagaagcga tgggaacgat\n",
      "      301 gtaatccatg aatacagaag attcaattga aaaagatcct atgatccatt gggaaggatg\n",
      "      361 gcggaacgaa ccagagacca attcatctat tctgaaaagt gataaactaa tcctataaaa\n",
      "      421 ctaaaataga tattgaaaga gtaaatattc gcccgcgaaa attccttttt tttttaaatt\n",
      "      481 gctcatattt tattttagca atgcaatcta ataaaatata tctatacaaa aaaataaaga\n",
      "      541 caaactatat atataatata tttcaaattt ccttatatat ccaaatataa aaatatctaa\n",
      "      601 taaattagat gaatatcaaa gaatctattg atttagtgta ttattaaatg tatatcttaa\n",
      "      661 ttcaatatta ttattctatt catttttatt cattttcaat tttataatat attaatctat\n",
      "      721 atattaattt ataattctat tctaattcga attcaatttt taaatattca tattcaatta\n",
      "      781 aaattgaaat tttttcattc gcgaggagcc ggatgagaag aaactctcat gtccggttct\n",
      "      841 gtagtagaga tggaattaag aaaaaaccat caactataac cccaagagaa ccaga\n",
      "//\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "text = handle.read()\n",
    "print(text)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "In this case, we are just getting the raw records. To get the records in\n",
    "a more Python-friendly form, we can use `Bio.SeqIO` to parse the GenBank\n",
    "data into `SeqRecord` objects, including `SeqFeature` objects (see\n",
    "Chapter \\[chapter:Bio.SeqIO\\]):\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from Bio import SeqIO\n",
    "handle = Entrez.efetch(db=\"nuccore\", id=gi_str, rettype=\"gb\", retmode=\"text\")\n",
    "records = SeqIO.parse(handle, \"gb\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "We can now step through the records and look at the information we are\n",
    "interested in:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "HQ621368, length 399, with 3 features\n",
      "HM041482, length 1197, with 3 features\n",
      "HM041481, length 1200, with 3 features\n",
      "HM041480, length 1153, with 3 features\n",
      "HM041479, length 1197, with 3 features\n",
      "HM041478, length 1187, with 3 features\n",
      "HM041477, length 1197, with 3 features\n",
      "HM041476, length 1205, with 3 features\n",
      "HM041474, length 1163, with 3 features\n",
      "HM041473, length 1203, with 3 features\n",
      "HM041472, length 1182, with 3 features\n",
      "HM041469, length 1189, with 3 features\n",
      "HM041468, length 1202, with 3 features\n",
      "HM041467, length 1199, with 3 features\n",
      "HM041466, length 1205, with 3 features\n",
      "HM041465, length 1190, with 3 features\n",
      "HM041464, length 1184, with 3 features\n",
      "AY851612, length 892, with 3 features\n",
      "AY851611, length 881, with 3 features\n",
      "AF191661, length 895, with 3 features\n"
     ]
    }
   ],
   "source": [
    "for record in records:\n",
    "    print(\"%s, length %i, with %i features\" \\\n",
    "    % (record.name, len(record), len(record.features)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Using these automated query retrieval functionality is a big plus over\n",
    "doing things by hand. Although the module should obey the NCBI’s max\n",
    "three queries per second rule, the NCBI have other recommendations like\n",
    "avoiding peak hours. See Section \\[sec:entrez-guidelines\\]. In\n",
    "particular, please note that for simplicity, this example does not use\n",
    "the WebEnv history feature. You should use this for any non-trivial\n",
    "search and download work, see Section [History and WebEnv](#Using-the-history-and-WebEnv).\n",
    "\n",
    "Finally, if plan to repeat your analysis, rather than downloading the\n",
    "files from the NCBI and parsing them immediately (as shown in this\n",
    "example), you should just download the records *once* and save them to\n",
    "your hard disk, and then parse the local file.\n",
    "\n",
    "### Finding the lineage of an organism\n",
    "\n",
    "Staying with a plant example, let’s now find the lineage of the\n",
    "Cypripedioideae orchid family. First, we search the Taxonomy database\n",
    "for Cypripedioideae, which yields exactly one NCBI taxonomy identifier:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['158330']"
      ]
     },
     "execution_count": 81,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"     # Always tell NCBI who you are\n",
    "handle = Entrez.esearch(db=\"Taxonomy\", term=\"Cypripedioideae\")\n",
    "record = Entrez.read(handle)\n",
    "record[\"IdList\"]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'158330'"
      ]
     },
     "execution_count": 82,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "record[\"IdList\"][0]\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Now, we use `efetch` to download this entry in the Taxonomy database,\n",
    "and then parse it:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "handle = Entrez.efetch(db=\"Taxonomy\", id=\"158330\", retmode=\"xml\")\n",
    "records = Entrez.read(handle)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Again, this record stores lots of information:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['PubDate', 'ScientificName', 'Division', 'MitoGeneticCode', 'GeneticCode', 'CreateDate', 'Rank', 'ParentTaxId', 'LineageEx', 'TaxId', 'Lineage', 'UpdateDate', 'OtherNames'])"
      ]
     },
     "execution_count": 84,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "records[0].keys()\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "We can get the lineage directly from this record:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; Asparagales; Orchidaceae'"
      ]
     },
     "execution_count": 85,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "records[0][\"Lineage\"]\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "The record data contains much more than just the information shown here\n",
    "- for example look under `LineageEx` instead of `Lineage` and you’ll get\n",
    "the NCBI taxon identifiers of the lineage entries too.\n",
    "\n",
    "Using the history and WebEnv\n",
    "---------------------------\n",
    "\n",
    "Often you will want to make a series of linked queries. Most typically,\n",
    "running a search, perhaps refining the search, and then retrieving\n",
    "detailed search results. You *can* do this by making a series of\n",
    "separate calls to Entrez. However, the NCBI prefer you to take advantage\n",
    "of their history support - for example combining ESearch and EFetch.\n",
    "\n",
    "Another typical use of the history support would be to combine EPost and\n",
    "EFetch. You use EPost to upload a list of identifiers, which starts a\n",
    "new history session. You then download the records with EFetch by\n",
    "referring to the session (instead of the identifiers).\n",
    "\n",
    "### Searching for and downloading sequences using the history\n",
    "\n",
    "Suppose we want to search and download all the *Opuntia* rpl16\n",
    "nucleotide sequences, and store them in a FASTA file. As shown in\n",
    "Section \\[sec:entrez-search-fetch-genbank\\], we can naively combine\n",
    "`Bio.Entrez.esearch()` to get a list of GI numbers, and then call\n",
    "`Bio.Entrez.efetch()` to download them all.\n",
    "\n",
    "However, the approved approach is to run the search with the history\n",
    "feature. Then, we can fetch the results by reference to the search\n",
    "results - which the NCBI can anticipate and cache.\n",
    "\n",
    "To do this, call `Bio.Entrez.esearch()` as normal, but with the\n",
    "additional argument of `usehistory=\"y\"`,\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"history.user@example.com\"\n",
    "search_handle = Entrez.esearch(db=\"nucleotide\",term=\"Opuntia[orgn] and rpl16\", usehistory=\"y\")\n",
    "search_results = Entrez.read(search_handle)\n",
    "search_handle.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "When you get the XML output back, it will still include the usual search\n",
    "results. However, you also get given two additional pieces of information, the\n",
    "```WebEnv``` session cookie, and the ```QueryKey```:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The WebEnv is NCID_1_946410500_130.14.18.34_9001_1452651901_1799213676_0MetA0_S_MegaStore_F_1\n",
      "The QueryKey is 1\n"
     ]
    }
   ],
   "source": [
    "gi_list = search_results[\"IdList\"]\n",
    "count = int(search_results[\"Count\"])\n",
    "assert count == len(gi_list)\n",
    "print(\"The WebEnv is {}\".format(search_results[\"WebEnv\"]))\n",
    "print(\"The QueryKey is {}\".format(search_results[\"QueryKey\"]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Having stored these values in variables <span>session\\_cookie</span> and\n",
    "<span>query\\_key</span> we can use them as parameters to\n",
    "`Bio.Entrez.efetch()` instead of giving the GI numbers as identifiers.\n",
    "\n",
    "While for small searches you might be OK downloading everything at once,\n",
    "it is better to download in batches. You use the <span>retstart</span>\n",
    "and <span>retmax</span> parameters to specify which range of search\n",
    "results you want returned (starting entry using zero-based counting, and\n",
    "maximum number of results to return). Sometimes you will get\n",
    "intermittent errors from Entrez, HTTPError 5XX, we use a try except\n",
    "pause retry block to address this. For example,\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "from Bio import Entrez\n",
    "import time\n",
    "try:\n",
    "    from urllib.error import HTTPError  # for Python 3\n",
    "except ImportError:\n",
    "    from urllib2 import HTTPError  # for Python 2\n",
    "batch_size = 3\n",
    "out_handle = open(\"orchid_rpl16.fasta\", \"w\")\n",
    "for start in range(0, count, batch_size):\n",
    "    end = min(count, start+batch_size)\n",
    "    print(\"Going to download record %i to %i\" % (start+1, end))\n",
    "    attempt = 1\n",
    "    while attempt <= 3:\n",
    "        try:\n",
    "            fetch_handle = Entrez.efetch(db=\"nucleotide\", rettype=\"fasta\", retmode=\"text\",\n",
    "                                         retstart=start, retmax=batch_size,\n",
    "                                         webenv=webenv, query_key=query_key)\n",
    "        except HTTPError as err:\n",
    "            if 500 <= err.code <= 599:\n",
    "                print(\"Received error from server %s\" % err)\n",
    "                print(\"Attempt %i of 3\" % attempt)\n",
    "                attempt += 1\n",
    "                time.sleep(15)\n",
    "            else:\n",
    "                raise\n",
    "    data = fetch_handle.read()\n",
    "    fetch_handle.close()\n",
    "    out_handle.write(data)\n",
    "out_handle.close()\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "For illustrative purposes, this example downloaded the FASTA records in\n",
    "batches of three. Unless you are downloading genomes or chromosomes, you\n",
    "would normally pick a larger batch size.\n",
    "\n",
    "### Searching for and downloading abstracts using the history\n",
    "\n",
    "Here is another history example, searching for papers published in the\n",
    "last year about the *Opuntia*, and then downloading them into a file in\n",
    "MedLine format:\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "from Bio import Entrez\n",
    "import time\n",
    "try:\n",
    "    from urllib.error import HTTPError  # for Python 3\n",
    "except ImportError:\n",
    "    from urllib2 import HTTPError  # for Python 2\n",
    "Entrez.email = \"history.user@example.com\"\n",
    "search_results = Entrez.read(Entrez.esearch(db=\"pubmed\",\n",
    "                                            term=\"Opuntia[ORGN]\",\n",
    "                                            reldate=365, datetype=\"pdat\",\n",
    "                                            usehistory=\"y\"))\n",
    "count = int(search_results[\"Count\"])\n",
    "print(\"Found %i results\" % count)\n",
    "\n",
    "batch_size = 10\n",
    "out_handle = open(\"recent_orchid_papers.txt\", \"w\")\n",
    "for start in range(0,count,batch_size):\n",
    "    end = min(count, start+batch_size)\n",
    "    print(\"Going to download record %i to %i\" % (start+1, end))\n",
    "    attempt = 1\n",
    "    while attempt <= 3:\n",
    "        try:\n",
    "            fetch_handle = Entrez.efetch(db=\"pubmed\",rettype=\"medline\",\n",
    "                                         retmode=\"text\",retstart=start,\n",
    "                                         retmax=batch_size,\n",
    "                                         webenv=search_results[\"WebEnv\"],\n",
    "                                         query_key=search_results[\"QueryKey\"])\n",
    "        except HTTPError as err:\n",
    "            if 500 <= err.code <= 599:\n",
    "                print(\"Received error from server %s\" % err)\n",
    "                print(\"Attempt %i of 3\" % attempt)\n",
    "                attempt += 1\n",
    "                time.sleep(15)\n",
    "            else:\n",
    "                raise\n",
    "    data = fetch_handle.read()\n",
    "    fetch_handle.close()\n",
    "    out_handle.write(data)\n",
    "out_handle.close()\n",
    "\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "At the time of writing, this gave 28 matches - but because this is a\n",
    "date dependent search, this will of course vary. As described in\n",
    "Section \\[subsec:entrez-and-medline\\] above, you can then use\n",
    "`Bio.Medline` to parse the saved records.\n",
    "\n",
    "### Searching for citations {#sec:elink-citations}\n",
    "\n",
    "Back in Section \\[sec:elink\\] we mentioned ELink can be used to search\n",
    "for citations of a given paper. Unfortunately this only covers journals\n",
    "indexed for PubMed Central (doing it for all the journals in PubMed\n",
    "would mean a lot more work for the NIH). Let’s try this for the\n",
    "Biopython PDB parser paper, PubMed ID 14630660:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['4595337',\n",
       " '4584387',\n",
       " '4520291',\n",
       " '4301084',\n",
       " '4173008',\n",
       " '4155247',\n",
       " '3879085',\n",
       " '3661355',\n",
       " '3531324',\n",
       " '3461403',\n",
       " '3394275',\n",
       " '3394243',\n",
       " '3312550',\n",
       " '3253748',\n",
       " '3161047',\n",
       " '3144279',\n",
       " '3122320',\n",
       " '3102222',\n",
       " '3096039',\n",
       " '3057020',\n",
       " '3036045',\n",
       " '2944279',\n",
       " '2902450',\n",
       " '2744707',\n",
       " '2705363',\n",
       " '2682512',\n",
       " '2483496',\n",
       " '2447749',\n",
       " '2098836',\n",
       " '2072961',\n",
       " '1933154',\n",
       " '1848001',\n",
       " '1192790',\n",
       " '1190160']"
      ]
     },
     "execution_count": 88,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio import Entrez\n",
    "Entrez.email = \"A.N.Other@example.com\"\n",
    "pmid = \"14630660\"\n",
    "results = Entrez.read(Entrez.elink(dbfrom=\"pubmed\", db=\"pmc\",\n",
    "LinkName=\"pubmed_pmc_refs\", from_uid=pmid))\n",
    "pmc_ids = [link[\"Id\"] for link in results[0][\"LinkSetDb\"][0][\"Link\"]]\n",
    "pmc_ids"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Great - eleven articles. But why hasn’t the Biopython application note\n",
    "been found (PubMed ID 19304878)? Well, as you might have guessed from\n",
    "the variable names, there are not actually PubMed IDs, but PubMed\n",
    "Central IDs. Our application note is the third citing paper in that\n",
    "list, PMCID 2682512.\n",
    "\n",
    "So, what if (like me) you’d rather get back a list of PubMed IDs? Well\n",
    "we can call ELink again to translate them. This becomes a two step\n",
    "process, so by now you should expect to use the history feature to\n",
    "accomplish it (Section [History and WebEnv](#Using-the-history-and-WebEnv)).\n",
    "\n",
    "But first, taking the more straightforward approach of making a second\n",
    "(separate) call to ELink:\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['26439842',\n",
       " '26306092',\n",
       " '26288158',\n",
       " '25420233',\n",
       " '24930144',\n",
       " '24849577',\n",
       " '24267035',\n",
       " '23717802',\n",
       " '23300419',\n",
       " '22784991',\n",
       " '22564897',\n",
       " '22553365',\n",
       " '22479120',\n",
       " '22361291',\n",
       " '21801404',\n",
       " '21637529',\n",
       " '21521828',\n",
       " '21500218',\n",
       " '21471012',\n",
       " '21467571',\n",
       " '20813068',\n",
       " '20607693',\n",
       " '20525384',\n",
       " '19698094',\n",
       " '19450287',\n",
       " '19304878',\n",
       " '18645234',\n",
       " '18502776',\n",
       " '18052533',\n",
       " '17888163',\n",
       " '17567620',\n",
       " '17397254',\n",
       " '16095538',\n",
       " '15985178']"
      ]
     },
     "execution_count": 89,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "results2 = Entrez.read(Entrez.elink(dbfrom=\"pmc\", db=\"pubmed\", LinkName=\"pmc_pubmed\",\n",
    "from_uid=\",\".join(pmc_ids)))\n",
    "pubmed_ids = [link[\"Id\"] for link in results2[0][\"LinkSetDb\"][0][\"Link\"]]\n",
    "pubmed_ids\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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