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__init__.py
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__init__.py
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# Copyright 1999-2000 by Jeffrey Chang. All rights reserved.
# Copyright 2008 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Provides code to access NCBI over the WWW.
The main Entrez web page is available at:
http://www.ncbi.nlm.nih.gov/Entrez/
A list of the Entrez utilities is available at:
http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
Variables:
email Set the Entrez email parameter (default is not set).
tool Set the Entrez tool parameter (default is biopython).
Functions:
efetch Retrieves records in the requested format from a list of one or
more primary IDs or from the user's environment
epost Posts a file containing a list of primary IDs for future use in
the user's environment to use with subsequent search strategies
esearch Searches and retrieves primary IDs (for use in EFetch, ELink,
and ESummary) and term translations and optionally retains
results for future use in the user's environment.
elink Checks for the existence of an external or Related Articles link
from a list of one or more primary IDs. Retrieves primary IDs
and relevancy scores for links to Entrez databases or Related
Articles; creates a hyperlink to the primary LinkOut provider
for a specific ID and database, or lists LinkOut URLs
and Attributes for multiple IDs.
einfo Provides field index term counts, last update, and available
links for each database.
esummary Retrieves document summaries from a list of primary IDs or from
the user's environment.
egquery Provides Entrez database counts in XML for a single search
using Global Query.
espell Retrieves spelling suggestions.
read Parses the XML results returned by any of the above functions.
Typical usage is:
>>> handle = Entrez.einfo() # or esearch, efetch, ...
>>> record = Entrez.read(handle)
where record is now a Python dictionary or list.
_open Internally used function.
"""
import urllib, urllib2, time, warnings
import os.path
email = None
tool = "biopython"
# XXX retmode?
def epost(db, **keywds):
"""Post a file of identifiers for future use.
Posts a file containing a list of UIs for future use in the user's
environment to use with subsequent search strategies.
See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html
Return a handle to the results.
Raises an IOError exception if there's a network error.
"""
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi'
variables = {'db' : db}
variables.update(keywds)
return _open(cgi, variables, post=False)
def efetch(db, **keywds):
"""Fetches Entrez results which are returned as a handle.
EFetch retrieves records in the requested format from a list of one or
more UIs or from user's environment.
See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
Return a handle to the results.
Raises an IOError exception if there's a network error.
Short example:
from Bio import Entrez
handle = Entrez.efetch(db="nucleotide", id="57240072", rettype="gb")
print handle.read()
"""
for key in keywds:
if key.lower()=="rettype" and keywds[key].lower()=="genbank":
warnings.warn('As of Easter 2009, Entrez EFetch no longer '
'supports the unofficial return type "genbank", '
'use "gb" or "gp" instead.', DeprecationWarning)
if db.lower()=="protein":
keywds[key] = "gp" #GenPept
else:
keywds[key] = "gb" #GenBank
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
variables = {'db' : db}
variables.update(keywds)
return _open(cgi, variables)
def esearch(db, term, **keywds):
"""ESearch runs an Entrez search and returns a handle to the results.
ESearch searches and retrieves primary IDs (for use in EFetch, ELink
and ESummary) and term translations, and optionally retains results
for future use in the user's environment.
See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
Return a handle to the results which are always in XML format.
Raises an IOError exception if there's a network error.
Short example:
from Bio import Entez
handle = Entrez.esearch(db="nucleotide", retmax=10, term="Opuntia")
record = Entrez.read(handle)
print record["Count"]
print record["IdList"]
"""
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
variables = {'db' : db,
'term' : term}
variables.update(keywds)
return _open(cgi, variables)
def elink(**keywds):
"""ELink checks for linked external articles and returns a handle.
ELink checks for the existence of an external or Related Articles link
from a list of one or more primary IDs; retrieves IDs and relevancy
scores for links to Entrez databases or Related Articles; creates a
hyperlink to the primary LinkOut provider for a specific ID and
database, or lists LinkOut URLs and attributes for multiple IDs.
See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html
Return a handle to the results, by default in XML format.
Raises an IOError exception if there's a network error.
"""
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'
variables = {}
variables.update(keywds)
return _open(cgi, variables)
def einfo(**keywds):
"""EInfo returns a summary of the Entez databases as a results handle.
EInfo provides field names, index term counts, last update, and
available links for each Entrez database.
See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html
Return a handle to the results, by default in XML format.
Raises an IOError exception if there's a network error.
Short example:
from Bio import Entrez
record = Entrez.read(Entrez.einfo())
print record['DbList']
"""
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi'
variables = {}
variables.update(keywds)
return _open(cgi, variables)
def esummary(**keywds):
"""ESummary retrieves document summaries as a results handle.
ESummary retrieves document summaries from a list of primary IDs or
from the user's environment.
See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/esummary_help.html
Return a handle to the results, by default in XML format.
Raises an IOError exception if there's a network error.
"""
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi'
variables = {}
variables.update(keywds)
return _open(cgi, variables)
def egquery(**keywds):
"""EGQuery provides Entrez database counts for a global search.
EGQuery provides Entrez database counts in XML for a single search
using Global Query.
See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/egquery_help.html
Return a handle to the results in XML format.
Raises an IOError exception if there's a network error.
"""
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi'
variables = {}
variables.update(keywds)
return _open(cgi, variables)
def espell(**keywds):
"""ESpell retrieves spelling suggestions, returned in a results handle.
ESpell retrieves spelling suggestions, if available.
See the online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/espell_help.html
Return a handle to the results, by default in XML format.
Raises an IOError exception if there's a network error.
Short example:
from Bio import Entrez
record = Entrez.read(Entrez.espell(term="biopythooon"))
print record["Query"]
print record["CorrectedQuery"]
"""
cgi='http://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi'
variables = {}
variables.update(keywds)
return _open(cgi, variables)
def read(handle):
"""Parses an XML file from the NCBI Entrez Utilities into python objects.
This function parses an XML file created by NCBI's Entrez Utilities,
returning a multilevel data structure of Python lists and dictionaries.
Most XML files returned by NCBI's Entrez Utilities can be parsed by
this function, provided its DTD is available. Biopython includes the
DTDs for most commonly used Entrez Utilities.
Whereas the data structure seems to consist of generic Python lists,
dictionaries, strings, and so on, each of these is actually a class
derived from the base type. This allows us to store the attributes
(if any) of each element in a dictionary my_element.attributes, and
the tag name in my_element.tag.
"""
from Parser import DataHandler
DTDs = os.path.join(str(__path__[0]), "DTDs")
handler = DataHandler(DTDs)
record = handler.read(handle)
return record
def parse(handle):
from Parser import DataHandler
DTDs = os.path.join(str(__path__[0]), "DTDs")
handler = DataHandler(DTDs)
records = handler.parse(handle)
return records
def _open(cgi, params={}, post=False):
"""Helper function to build the URL and open a handle to it (PRIVATE).
Open a handle to Entrez. cgi is the URL for the cgi script to access.
params is a dictionary with the options to pass to it. Does some
simple error checking, and will raise an IOError if it encounters one.
This function also enforces the "up to three queries per second rule"
to avoid abusing the NCBI servers.
"""
# NCBI requirement: At most three queries per second.
# Equivalently, at least a third of second between queries
delay = 0.333333334
current = time.time()
wait = _open.previous + delay - current
if wait > 0:
time.sleep(wait)
_open.previous = current + wait
else:
_open.previous = current
# Remove None values from the parameters
for key, value in params.items():
if value is None:
del params[key]
# Tell Entrez that we are using Biopython (or whatever the user has
# specified explicitly in the parameters or by changing the default)
if not "tool" in params:
params["tool"] = tool
# Tell Entrez who we are
if not "email" in params:
if email!=None:
params["email"] = email
else:
warnings.warn("""
Email address is not specified.
To make use of NCBI's E-utilities, NCBI strongly recommends you to specify
your email address with each request. From June 1, 2010, this will be
mandatory. As an example, if your email address is A.N.Other@example.com, you
can specify it as follows:
from Bio import Entrez
Entrez.email = 'A.N.Other@example.com'
In case of excessive usage of the E-utilities, NCBI will attempt to contact
a user at the email address provided before blocking access to the
E-utilities.""", UserWarning)
# Open a handle to Entrez.
options = urllib.urlencode(params, doseq=True)
try:
if post:
#HTTP POST
handle = urllib2.urlopen(cgi, data=options)
else:
#HTTP GET
cgi += "?" + options
handle = urllib2.urlopen(cgi)
except urllib2.HTTPError, exception:
raise exception
return handle
_open.previous = 0