tests/ipyrad-manuscript-Loxodonta-ddrad.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# PE ddRAD data analysis with denovo and reference based assembly\n",
    "Data from \"Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant\"\n",
    "\n",
    "* http://onlinelibrary.wiley.com/doi/10.1002/ece3.3854/full?wol1URL=/doi/10.1002/ece3.3854/full&regionCode=US-NY&identityKey=34b23ec9-4666-4c37-8470-8448e64d6167\n",
    "\n",
    "## Other PE ddRAD datasets that could have been useful\n",
    "Ptychadena\n",
    "* http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190440#sec022\n",
    "\n",
    "Peromyscus (Munshi-South)\n",
    "\n",
    "Chinese sea bass (SRP094869)\n",
    "* Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus)\n",
    "* https://link.springer.com/article/10.1007/s10126-017-9786-0#Sec2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import ipyrad as ip\n",
    "import ipyrad.analysis as ipa\n",
    "import ipyparallel as ipp\n",
    "import pandas as pd\n",
    "import toyplot\n",
    "import glob\n",
    "import gzip\n",
    "\n",
    "\n",
    "## Ptychadena (Stephane)\n",
    "## * http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190440#sec022\n",
    "\n",
    "## Peromyscus (Munshi-South)\n",
    "\n",
    "## Chinese sea bass (SRP094869)\n",
    "## Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus)\n",
    "## * https://link.springer.com/article/10.1007/s10126-017-9786-0#Sec2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "conda install -c eaton-lab toytree\n",
    "conda install -c bioconda sra-tools entrez-direct"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "## Fetch the elephant reference genome\n",
    "mkdir ref\n",
    "wget ftp://ftp.broadinstitute.org/pub/assemblies/mammals/elephant/loxAfr3/assembly_supers.fasta.gz -o ref/assembly_supers.fasta.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "\n",
    "## Data from \"Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant\"\n",
    "## http://onlinelibrary.wiley.com/doi/10.1002/ece3.3854/full?wol1URL=/doi/10.1002/ece3.3854/full&regionCode=US-NY&identityKey=34b23ec9-4666-4c37-8470-8448e64d6167\n",
    "ipyrad --download SRP126637 raws/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['raws/LOC0310_SRR6371511.fastq.gz', 'raws/LOC0088_SRR6371521.fastq.gz', 'raws/LOC0311_SRR6371510.fastq.gz', 'raws/LOC0051_SRR6371516.fastq.gz', 'raws/LOC0037_SRR6371514.fastq.gz', 'raws/LOC0038_SRR6371513.fastq.gz', 'raws/LOC0040_SRR6371512.fastq.gz', 'raws/LOC0041_SRR6371519.fastq.gz', 'raws/LOC0050_SRR6371517.fastq.gz', 'raws/LOC0309_SRR6371508.fastq.gz', 'raws/LOC0151_SRR6371505.fastq.gz', 'raws/LOC0127_SRR6371502.fastq.gz', 'raws/LOC0279_SRR6371509.fastq.gz', 'raws/LOC0274_SRR6371506.fastq.gz', 'raws/LOC0049_SRR6371518.fastq.gz', 'raws/LOC0035_SRR6371515.fastq.gz', 'raws/LOC0121_SRR6371520.fastq.gz', 'raws/LOC0263_SRR6371507.fastq.gz', 'raws/LOC0122_SRR6371503.fastq.gz']\n",
      "LOC0310 535328\n",
      "LOC0088 2532764\n",
      "LOC0311 2381720\n",
      "LOC0051 2267296\n",
      "LOC0037 4639748\n",
      "LOC0038 4352988\n",
      "LOC0040 1516120\n",
      "LOC0041 2733056\n",
      "LOC0050 3633896\n",
      "LOC0309 2004280\n",
      "LOC0151 2005558\n",
      "LOC0127 482392\n",
      "LOC0279 5789736\n",
      "LOC0274 3165976\n",
      "LOC0049 2942484\n",
      "LOC0035 1812120\n",
      "LOC0121 450136\n",
      "LOC0263 5038456\n",
      "LOC0122 2266816\n"
     ]
    }
   ],
   "source": [
    "## R1 and R2 were concatenated in the SRA data files so we have to pull them apart.\n",
    "## This is probably not the most efficient way to do this, but it works.\n",
    "raws = glob.glob(\"raws/*\")\n",
    "print(raws)\n",
    "for r in raws:\n",
    "    name = r.split(\"/\")[1].split(\"_\")[0]\n",
    "    lines = gzip.open(r).readlines()\n",
    "    nlines = len(lines)/2\n",
    "    print(\"{} {}\".format(name, nlines))\n",
    "    with gzip.open(\"raws/{}_R1_.fastq.gz\".format(name), 'wb') as r1:\n",
    "        r1.write(\"\".join(lines[:nlines]))\n",
    "    with gzip.open(\"raws/{}_R2_.fastq.gz\".format(name), 'wb') as r2:\n",
    "        r2.write(\"\".join(lines[nlines:]))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "Fetching project data...\n",
    "           Run    spots mates      ScientificName SampleName\n",
    "0   SRR6371502   241196     0  Loxodonta cyclotis    LOC0127\n",
    "1   SRR6371503  1133408     0  Loxodonta cyclotis    LOC0122\n",
    "2   SRR6371505  1002779     0  Loxodonta cyclotis    LOC0151\n",
    "3   SRR6371506  1582988     0  Loxodonta cyclotis    LOC0274\n",
    "4   SRR6371507  2519228     0  Loxodonta cyclotis    LOC0263\n",
    "5   SRR6371508  1002140     0  Loxodonta cyclotis    LOC0309\n",
    "6   SRR6371509  2894868     0  Loxodonta cyclotis    LOC0279\n",
    "7   SRR6371510  1190860     0  Loxodonta cyclotis    LOC0311\n",
    "8   SRR6371511   267664     0  Loxodonta cyclotis    LOC0310\n",
    "9   SRR6371512   758060     0  Loxodonta cyclotis    LOC0040\n",
    "10  SRR6371513  2176494     0  Loxodonta cyclotis    LOC0038\n",
    "11  SRR6371514  2319874     0  Loxodonta cyclotis    LOC0037\n",
    "12  SRR6371515   906060     0  Loxodonta cyclotis    LOC0035\n",
    "13  SRR6371516  1133648     0  Loxodonta cyclotis    LOC0051\n",
    "14  SRR6371517  1816948     0  Loxodonta cyclotis    LOC0050\n",
    "15  SRR6371518  1471242     0  Loxodonta cyclotis    LOC0049\n",
    "16  SRR6371519  1366528     0  Loxodonta cyclotis    LOC0041\n",
    "17  SRR6371520   225068     0  Loxodonta cyclotis    LOC0121\n",
    "18  SRR6371521  1266382     0  Loxodonta cyclotis    LOC0088\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "             0          7                 8\n",
      "0   SRR6371521  LOC0088_a              Lope\n",
      "1   SRR6371520  LOC0121_a           Minkebe\n",
      "2   SRR6371519  LOC0041_a              Waka\n",
      "3   SRR6371518  LOC0049_a            Ivindo\n",
      "4   SRR6371517  LOC0050_b            Ivindo\n",
      "5   SRR6371516  LOC0051_a            Ivindo\n",
      "6   SRR6371515  LOC0035_a           Minkebe\n",
      "7   SRR6371514  LOC0037_a              Lope\n",
      "8   SRR6371513  LOC0038_a              Lope\n",
      "9   SRR6371512  LOC0040_a      Wonga Wongue\n",
      "10  SRR6371511  LOC0310_a  Moukalaba Doudou\n",
      "11  SRR6371510  LOC0311_a  Monts de Cristal\n",
      "12  SRR6371509  LOC0279_b     South Mulundu\n",
      "13  SRR6371508  LOC0309_a           Mayumba\n",
      "14  SRR6371507  LOC0263_a      Wonga Wongue\n",
      "15  SRR6371506  LOC0274_a            Loango\n",
      "16  SRR6371505  LOC0151_a  Moukalaba Doudou\n",
      "17  SRR6371503  LOC0122_a           Minkebe\n",
      "18  SRR6371502  LOC0127_a  Moukalaba Doudou\n"
     ]
    }
   ],
   "source": [
    "df = pd.DataFrame([x.split(\"\\t\") for x in \"\"\"SRR6371521\tSAMN08167496\tLOC0088\tWG011\t178\t95\tSRX3466825\tLOC0088_a\tLope\n",
    "SRR6371520\tSAMN08167497\tLOC0121\tWG012\t31\t16\tSRX3466826\tLOC0121_a\tMinkebe\n",
    "SRR6371519\tSAMN08167492\tLOC0041\tWG005\t192\t102\tSRX3466827\tLOC0041_a\tWaka\n",
    "SRR6371518\tSAMN08167493\tLOC0049\tWG008\t207\t110\tSRX3466828\tLOC0049_a\tIvindo\n",
    "SRR6371517\tSAMN08167494\tLOC0050\tWG009\t256\t135\tSRX3466829\tLOC0050_b\tIvindo\n",
    "SRR6371516\tSAMN08167495\tLOC0051\tWG010\t160\t85\tSRX3466830\tLOC0051_a\tIvindo\n",
    "SRR6371515\tSAMN08167488\tLOC0035\tWG001\t127\t69\tSRX3466831\tLOC0035_a\tMinkebe\n",
    "SRR6371514\tSAMN08167489\tLOC0037\tWG002\t327\t175\tSRX3466832\tLOC0037_a\tLope\n",
    "SRR6371513\tSAMN08167490\tLOC0038\tWG003\t307\t164\tSRX3466833\tLOC0038_a\tLope\n",
    "SRR6371512\tSAMN08167491\tLOC0040\tWG004\t106\t56\tSRX3466834\tLOC0040_a\tWonga Wongue\n",
    "SRR6371511\tSAMN08167506\tLOC0310\tWG023\t37\t20\tSRX3466835\tLOC0310_a\tMoukalaba Doudou\n",
    "SRR6371510\tSAMN08167507\tLOC0311\tWG024\t168\t89\tSRX3466836\tLOC0311_a\tMonts de Cristal\n",
    "SRR6371509\tSAMN08167504\tLOC0279\tWG020\t408\t215\tSRX3466837\tLOC0279_b\tSouth Mulundu\n",
    "SRR6371508\tSAMN08167505\tLOC0309\tWG022\t141\t75\tSRX3466838\tLOC0309_a\tMayumba\n",
    "SRR6371507\tSAMN08167502\tLOC0263\tWG018\t355\t188\tSRX3466839\tLOC0263_a\tWonga Wongue\n",
    "SRR6371506\tSAMN08167503\tLOC0274\tWG019\t223\t117\tSRX3466840\tLOC0274_a\tLoango\n",
    "SRR6371505\tSAMN08167500\tLOC0151\tWG015\t141\t71\tSRX3466841\tLOC0151_a\tMoukalaba Doudou\n",
    "SRR6371503\tSAMN08167498\tLOC0122\tWG013\t159\t85\tSRX3466843\tLOC0122_a\tMinkebe\n",
    "SRR6371502\tSAMN08167499\tLOC0127\tWG014\t34\t18\tSRX3466844\tLOC0127_a\tMoukalaba Doudou\"\"\".split(\"\\n\")])\n",
    "\n",
    "## Just get the sequence identifier, the sample name, and the sample location\n",
    "df = df.iloc[:, [0,7,8]]\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Launch the cluster by running this command on the command line:\n",
    "\n",
    "    ipcluster start --n=19 --daemonize"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## connect to cluster and check if all the engines are running\n",
    "ipyclient = ipp.Client()\n",
    "ipyclient.ids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "New Assembly: Loxodonta\n"
     ]
    }
   ],
   "source": [
    "data = ip.Assembly(\"Loxodonta\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0   assembly_name               Loxodonta                                    \n",
      "1   project_dir                 ./ddrad-denovo                               \n",
      "2   raw_fastq_path                                                           \n",
      "3   barcodes_path                                                            \n",
      "4   sorted_fastq_path           ./raws/*_.fastq                              \n",
      "5   assembly_method             denovo                                       \n",
      "6   reference_sequence                                                       \n",
      "7   datatype                    pairddrad                                    \n",
      "8   restriction_overhang        ('TGCAG', 'CATGC')                           \n",
      "9   max_low_qual_bases          5                                            \n",
      "10  phred_Qscore_offset         33                                           \n",
      "11  mindepth_statistical        6                                            \n",
      "12  mindepth_majrule            6                                            \n",
      "13  maxdepth                    10000                                        \n",
      "14  clust_threshold             0.9                                          \n",
      "15  max_barcode_mismatch        0                                            \n",
      "16  filter_adapters             2                                            \n",
      "17  filter_min_trim_len         35                                           \n",
      "18  max_alleles_consens         2                                            \n",
      "19  max_Ns_consens              (5, 5)                                       \n",
      "20  max_Hs_consens              (5, 5)                                       \n",
      "21  min_samples_locus           4                                            \n",
      "22  max_SNPs_locus              (20, 20)                                     \n",
      "23  max_Indels_locus            (8, 8)                                       \n",
      "24  max_shared_Hs_locus         0.5                                          \n",
      "25  trim_reads                  (0, 0, 0, 0)                                 \n",
      "26  trim_loci                   (0, 0, 0, 0)                                 \n",
      "27  output_formats              ['G', 'a', 'g', 'k', 'm', 'l', 'n', 'p', 's', 'u', 't', 'v']\n",
      "28  pop_assign_file                                                          \n"
     ]
    }
   ],
   "source": [
    "## set parameters\n",
    "data.set_params(\"project_dir\", \"ddrad-denovo\")\n",
    "data.set_params(\"sorted_fastq_path\", \"raws/*_.fastq\")\n",
    "data.set_params(\"datatype\", \"pairddrad\")\n",
    "data.set_params(\"restriction_overhang\", (\"TGCAG\", \"CATGC\"))\n",
    "data.set_params(\"clust_threshold\", \"0.90\")\n",
    "data.set_params(\"filter_adapters\", \"2\")\n",
    "data.set_params(\"max_Hs_consens\", (5, 5))\n",
    "data.set_params(\"trim_loci\", (0, 0, 0, 0))\n",
    "data.set_params(\"output_formats\", \"*\")\n",
    "\n",
    "## see/print all parameters\n",
    "data.get_params()\n",
    "data.write_params(force=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Assembly: Loxodonta\n",
      "    Skipping: 19 Samples already found in Assembly Loxodonta.\n",
      "    (can overwrite with force argument)    \n",
      "[####################] 100%  processing reads      | 0:00:02 | s2 | \n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n",
      "  found an error in step2; see ipyrad_log.txt\n"
     ]
    }
   ],
   "source": [
    "data.run(\"12\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
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       "        vertical-align: top;\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>state</th>\n",
       "      <th>reads_raw</th>\n",
       "      <th>reads_passed_filter</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>LOC0035_SRR6371515</th>\n",
       "      <td>2</td>\n",
       "      <td>906060</td>\n",
       "      <td>905955</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0037_SRR6371514</th>\n",
       "      <td>2</td>\n",
       "      <td>2319874</td>\n",
       "      <td>2319590</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0038_SRR6371513</th>\n",
       "      <td>2</td>\n",
       "      <td>2176494</td>\n",
       "      <td>2176182</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0040_SRR6371512</th>\n",
       "      <td>2</td>\n",
       "      <td>758060</td>\n",
       "      <td>757942</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0041_SRR6371519</th>\n",
       "      <td>2</td>\n",
       "      <td>1366528</td>\n",
       "      <td>1366341</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0049_SRR6371518</th>\n",
       "      <td>2</td>\n",
       "      <td>1471242</td>\n",
       "      <td>1471081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0050_SRR6371517</th>\n",
       "      <td>2</td>\n",
       "      <td>1816948</td>\n",
       "      <td>1816737</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0051_SRR6371516</th>\n",
       "      <td>2</td>\n",
       "      <td>1133648</td>\n",
       "      <td>1133530</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0088_SRR6371521</th>\n",
       "      <td>2</td>\n",
       "      <td>1266382</td>\n",
       "      <td>1266181</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0121_SRR6371520</th>\n",
       "      <td>2</td>\n",
       "      <td>225068</td>\n",
       "      <td>225031</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0122_SRR6371503</th>\n",
       "      <td>2</td>\n",
       "      <td>1133408</td>\n",
       "      <td>1133305</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0127_SRR6371502</th>\n",
       "      <td>2</td>\n",
       "      <td>241196</td>\n",
       "      <td>241079</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0151_SRR6371505</th>\n",
       "      <td>2</td>\n",
       "      <td>1002779</td>\n",
       "      <td>1002680</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0263_SRR6371507</th>\n",
       "      <td>2</td>\n",
       "      <td>2519228</td>\n",
       "      <td>2518887</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0274_SRR6371506</th>\n",
       "      <td>2</td>\n",
       "      <td>1582988</td>\n",
       "      <td>1582731</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0279_SRR6371509</th>\n",
       "      <td>2</td>\n",
       "      <td>2894868</td>\n",
       "      <td>2894465</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0309_SRR6371508</th>\n",
       "      <td>2</td>\n",
       "      <td>1002140</td>\n",
       "      <td>1002002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0310_SRR6371511</th>\n",
       "      <td>2</td>\n",
       "      <td>267664</td>\n",
       "      <td>267643</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LOC0311_SRR6371510</th>\n",
       "      <td>2</td>\n",
       "      <td>1190860</td>\n",
       "      <td>1190747</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                    state  reads_raw  reads_passed_filter\n",
       "LOC0035_SRR6371515      2     906060               905955\n",
       "LOC0037_SRR6371514      2    2319874              2319590\n",
       "LOC0038_SRR6371513      2    2176494              2176182\n",
       "LOC0040_SRR6371512      2     758060               757942\n",
       "LOC0041_SRR6371519      2    1366528              1366341\n",
       "LOC0049_SRR6371518      2    1471242              1471081\n",
       "LOC0050_SRR6371517      2    1816948              1816737\n",
       "LOC0051_SRR6371516      2    1133648              1133530\n",
       "LOC0088_SRR6371521      2    1266382              1266181\n",
       "LOC0121_SRR6371520      2     225068               225031\n",
       "LOC0122_SRR6371503      2    1133408              1133305\n",
       "LOC0127_SRR6371502      2     241196               241079\n",
       "LOC0151_SRR6371505      2    1002779              1002680\n",
       "LOC0263_SRR6371507      2    2519228              2518887\n",
       "LOC0274_SRR6371506      2    1582988              1582731\n",
       "LOC0279_SRR6371509      2    2894868              2894465\n",
       "LOC0309_SRR6371508      2    1002140              1002002\n",
       "LOC0310_SRR6371511      2     267664               267643\n",
       "LOC0311_SRR6371510      2    1190860              1190747"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## access the stats of the assembly (so far) from the .stats attribute\n",
    "data.stats"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Assembly: Loxodonta\n",
      "[####################] 100%  dereplicating         | 0:00:22 | s3 | \n",
      "[####################] 100%  clustering            | 0:06:02 | s3 | \n",
      "[####################] 100%  building clusters     | 0:00:21 | s3 | \n",
      "[####################] 100%  chunking              | 0:00:03 | s3 | \n",
      "[####################] 100%  aligning              | 0:20:57 | s3 | \n",
      "[####################] 100%  concatenating         | 0:00:13 | s3 | \n",
      "[####################] 100%  inferring [H, E]      | 0:01:48 | s4 | \n",
      "[####################] 100%  calculating depths    | 0:00:04 | s5 | \n",
      "[####################] 100%  chunking clusters     | 0:00:04 | s5 | \n",
      "[####################] 100%  consens calling       | 0:03:03 | s5 | \n",
      "[####################] 100%  concat/shuffle input  | 0:00:04 | s6 | \n",
      "[####################] 100%  clustering across     | 0:02:13 | s6 | \n",
      "[####################] 100%  building clusters     | 0:00:03 | s6 | \n",
      "[####################] 100%  aligning clusters     | 0:01:07 | s6 | \n",
      "[####################] 100%  database indels       | 0:00:07 | s6 | \n",
      "[####################] 100%  indexing clusters     | 0:00:04 | s6 | \n",
      "[####################] 100%  building database     | 0:00:13 | s6 | \n",
      "[####################] 100%  filtering loci        | 0:00:10 | s7 | \n",
      "[####################] 100%  building loci/stats   | 0:00:03 | s7 | \n",
      "[####################] 100%  building alleles      | 0:00:04 | s7 | \n",
      "[####################] 100%  building vcf file     | 0:00:07 | s7 | \n",
      "[####################] 100%  writing vcf file      | 0:00:00 | s7 | \n",
      "[####################] 100%  building arrays       | 0:00:04 | s7 | \n",
      "[####################] 100%  writing outfiles      | 0:00:06 | s7 | \n",
      "Outfiles written to: ~/ipyrad/test-data/manu-ddrad-elephants/ddrad-denovo/Loxodonta_outfiles\n",
      "\n"
     ]
    }
   ],
   "source": [
    "## run steps 3-6 of the assembly\n",
    "data.run(\"34567\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "submitted 4 structure jobs [quick-K-2]\n",
      "submitted 4 structure jobs [quick-K-3]\n",
      "submitted 4 structure jobs [quick-K-4]\n",
      "submitted 4 structure jobs [quick-K-5]\n",
      "submitted 4 structure jobs [quick-K-6]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "kvalues = [2, 3, 4, 5, 6]\n",
    "s = ipa.structure(\n",
    "    name=\"quick\",\n",
    "    workdir=\"./analysis-structure\",\n",
    "    data=\"./ddrad-denovo/Loxodonta_outfiles/Loxodonta.ustr\",\n",
    "    )\n",
    "\n",
    "## set main params (use much larger values in a real analysis)\n",
    "s.mainparams.burnin = 1000\n",
    "s.mainparams.numreps = 5000\n",
    "\n",
    "## submit N replicates of each test to run on parallel client\n",
    "for kpop in kvalues:\n",
    "    s.run(kpop=kpop, nreps=4, ipyclient=ipyclient)\n",
    "\n",
    "## wait for parallel jobs to finish\n",
    "ipyclient.wait()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Nreps</th>\n",
       "      <th>deltaK</th>\n",
       "      <th>estLnProbMean</th>\n",
       "      <th>estLnProbStdev</th>\n",
       "      <th>lnPK</th>\n",
       "      <th>lnPPK</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4</td>\n",
       "      <td>0.000</td>\n",
       "      <td>-5.503e+05</td>\n",
       "      <td>5.116e+05</td>\n",
       "      <td>0.000</td>\n",
       "      <td>0.000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>3.163</td>\n",
       "      <td>-3.206e+05</td>\n",
       "      <td>3.185e+05</td>\n",
       "      <td>229741.725</td>\n",
       "      <td>1.007e+06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4</td>\n",
       "      <td>0.455</td>\n",
       "      <td>-1.098e+06</td>\n",
       "      <td>6.932e+05</td>\n",
       "      <td>-777577.375</td>\n",
       "      <td>3.152e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>4</td>\n",
       "      <td>1.264</td>\n",
       "      <td>-1.560e+06</td>\n",
       "      <td>6.283e+05</td>\n",
       "      <td>-462336.825</td>\n",
       "      <td>7.943e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>4</td>\n",
       "      <td>0.000</td>\n",
       "      <td>-1.229e+06</td>\n",
       "      <td>1.059e+06</td>\n",
       "      <td>331935.450</td>\n",
       "      <td>0.000e+00</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Nreps  deltaK  estLnProbMean  estLnProbStdev        lnPK      lnPPK\n",
       "2      4   0.000     -5.503e+05       5.116e+05       0.000  0.000e+00\n",
       "3      4   3.163     -3.206e+05       3.185e+05  229741.725  1.007e+06\n",
       "4      4   0.455     -1.098e+06       6.932e+05 -777577.375  3.152e+05\n",
       "5      4   1.264     -1.560e+06       6.283e+05 -462336.825  7.943e+05\n",
       "6      4   0.000     -1.229e+06       1.059e+06  331935.450  0.000e+00"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## return the evanno table (deltaK) for best K \n",
    "etable = s.get_evanno_table(kvalues)\n",
    "etable"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{2:                             0          1\n",
      "LOC0035_SRR6371515  2.510e-01  7.490e-01\n",
      "LOC0037_SRR6371514  4.995e-01  5.005e-01\n",
      "LOC0038_SRR6371513  4.972e-01  5.027e-01\n",
      "LOC0040_SRR6371512  1.000e-03  9.990e-01\n",
      "LOC0041_SRR6371519  5.835e-01  4.165e-01\n",
      "LOC0049_SRR6371518  9.995e-01  5.000e-04\n",
      "LOC0050_SRR6371517  1.000e+00  0.000e+00\n",
      "LOC0051_SRR6371516  9.988e-01  1.300e-03\n",
      "LOC0088_SRR6371521  3.583e-01  6.418e-01\n",
      "LOC0121_SRR6371520  2.000e-03  9.980e-01\n",
      "LOC0122_SRR6371503  2.700e-03  9.972e-01\n",
      "LOC0127_SRR6371502  1.512e-01  8.487e-01\n",
      "LOC0151_SRR6371505  2.515e-01  7.485e-01\n",
      "LOC0263_SRR6371507  8.000e-04  9.992e-01\n",
      "LOC0274_SRR6371506  2.507e-01  7.492e-01\n",
      "LOC0279_SRR6371509  4.995e-01  5.005e-01\n",
      "LOC0309_SRR6371508  3.872e-01  6.128e-01\n",
      "LOC0310_SRR6371511  2.500e-01  7.500e-01\n",
      "LOC0311_SRR6371510  4.992e-01  5.008e-01, 3:                             0          1          2\n",
      "LOC0035_SRR6371515  1.500e-03  9.800e-02  9.005e-01\n",
      "LOC0037_SRR6371514  3.000e-04  9.995e-01  3.000e-04\n",
      "LOC0038_SRR6371513  3.000e-04  9.995e-01  3.000e-04\n",
      "LOC0040_SRR6371512  2.382e-01  2.500e-01  5.117e-01\n",
      "LOC0041_SRR6371519  1.500e-03  4.993e-01  4.993e-01\n",
      "LOC0049_SRR6371518  9.992e-01  5.000e-04  3.000e-04\n",
      "LOC0050_SRR6371517  1.000e+00  0.000e+00  0.000e+00\n",
      "LOC0051_SRR6371516  9.998e-01  0.000e+00  3.000e-04\n",
      "LOC0088_SRR6371521  2.520e-01  7.248e-01  2.320e-02\n",
      "LOC0121_SRR6371520  2.000e-03  2.510e-01  7.470e-01\n",
      "LOC0122_SRR6371503  2.500e-01  2.502e-01  4.997e-01\n",
      "LOC0127_SRR6371502  1.203e-01  3.405e-01  5.392e-01\n",
      "LOC0151_SRR6371505  5.620e-02  4.430e-01  5.007e-01\n",
      "LOC0263_SRR6371507  3.200e-03  2.300e-03  9.945e-01\n",
      "LOC0274_SRR6371506  2.720e-01  2.513e-01  4.767e-01\n",
      "LOC0279_SRR6371509  9.000e-03  2.617e-01  7.293e-01\n",
      "LOC0309_SRR6371508  7.132e-01  3.800e-03  2.830e-01\n",
      "LOC0310_SRR6371511  3.850e-02  2.833e-01  6.783e-01\n",
      "LOC0311_SRR6371510  4.722e-01  2.515e-01  2.762e-01, 4:                         0          1      2          3\n",
      "LOC0035_SRR6371515  0.010  1.950e-02  0.726  2.447e-01\n",
      "LOC0037_SRR6371514  0.001  9.900e-01  0.007  1.800e-03\n",
      "LOC0038_SRR6371513  0.001  9.828e-01  0.013  3.000e-03\n",
      "LOC0040_SRR6371512  0.002  6.850e-02  0.454  4.760e-01\n",
      "LOC0041_SRR6371519  0.052  4.800e-03  0.446  4.980e-01\n",
      "LOC0049_SRR6371518  0.994  2.000e-03  0.003  1.000e-03\n",
      "LOC0050_SRR6371517  0.998  3.000e-04  0.002  3.000e-04\n",
      "LOC0051_SRR6371516  0.995  8.000e-04  0.003  1.500e-03\n",
      "LOC0088_SRR6371521  0.067  6.450e-01  0.242  4.650e-02\n",
      "LOC0121_SRR6371520  0.028  4.700e-01  0.471  3.070e-02\n",
      "LOC0122_SRR6371503  0.038  2.665e-01  0.254  4.415e-01\n",
      "LOC0127_SRR6371502  0.015  2.355e-01  0.299  4.500e-01\n",
      "LOC0151_SRR6371505  0.382  2.782e-01  0.265  7.570e-02\n",
      "LOC0263_SRR6371507  0.011  2.750e-02  0.536  4.257e-01\n",
      "LOC0274_SRR6371506  0.003  2.515e-01  0.717  2.850e-02\n",
      "LOC0279_SRR6371509  0.004  2.525e-01  0.249  4.945e-01\n",
      "LOC0309_SRR6371508  0.186  8.700e-03  0.731  7.500e-02\n",
      "LOC0310_SRR6371511  0.044  1.450e-02  0.025  9.158e-01\n",
      "LOC0311_SRR6371510  0.034  2.054e-01  0.703  5.760e-02, 5:                         0      1      2      3      4\n",
      "LOC0035_SRR6371515  0.071  0.043  0.854  0.008  0.025\n",
      "LOC0037_SRR6371514  0.004  0.004  0.005  0.002  0.986\n",
      "LOC0038_SRR6371513  0.009  0.004  0.006  0.005  0.976\n",
      "LOC0040_SRR6371512  0.435  0.260  0.259  0.003  0.043\n",
      "LOC0041_SRR6371519  0.020  0.239  0.466  0.029  0.245\n",
      "LOC0049_SRR6371518  0.006  0.005  0.009  0.965  0.015\n",
      "LOC0050_SRR6371517  0.007  0.003  0.013  0.974  0.003\n",
      "LOC0051_SRR6371516  0.009  0.005  0.018  0.965  0.003\n",
      "LOC0088_SRR6371521  0.035  0.630  0.043  0.014  0.276\n",
      "LOC0121_SRR6371520  0.030  0.263  0.674  0.015  0.018\n",
      "LOC0122_SRR6371503  0.732  0.181  0.019  0.020  0.049\n",
      "LOC0127_SRR6371502  0.408  0.042  0.131  0.077  0.341\n",
      "LOC0151_SRR6371505  0.478  0.017  0.478  0.019  0.009\n",
      "LOC0263_SRR6371507  0.020  0.736  0.012  0.011  0.221\n",
      "LOC0274_SRR6371506  0.561  0.029  0.336  0.012  0.061\n",
      "LOC0279_SRR6371509  0.198  0.297  0.013  0.019  0.473\n",
      "LOC0309_SRR6371508  0.300  0.063  0.377  0.058  0.203\n",
      "LOC0310_SRR6371511  0.015  0.298  0.598  0.011  0.076\n",
      "LOC0311_SRR6371510  0.430  0.473  0.016  0.009  0.073, 6:                         0      1      2      3      4      5\n",
      "LOC0035_SRR6371515  0.262  0.005  0.236  0.225  0.015  0.258\n",
      "LOC0037_SRR6371514  0.007  0.001  0.002  0.005  0.982  0.003\n",
      "LOC0038_SRR6371513  0.004  0.001  0.002  0.003  0.986  0.003\n",
      "LOC0040_SRR6371512  0.875  0.017  0.012  0.068  0.023  0.005\n",
      "LOC0041_SRR6371519  0.271  0.011  0.254  0.183  0.003  0.278\n",
      "LOC0049_SRR6371518  0.006  0.942  0.013  0.017  0.015  0.006\n",
      "LOC0050_SRR6371517  0.006  0.951  0.012  0.025  0.004  0.002\n",
      "LOC0051_SRR6371516  0.010  0.909  0.021  0.042  0.003  0.016\n",
      "LOC0088_SRR6371521  0.143  0.020  0.137  0.028  0.415  0.257\n",
      "LOC0121_SRR6371520  0.242  0.017  0.010  0.662  0.058  0.012\n",
      "LOC0122_SRR6371503  0.126  0.091  0.210  0.363  0.068  0.142\n",
      "LOC0127_SRR6371502  0.192  0.028  0.078  0.242  0.035  0.426\n",
      "LOC0151_SRR6371505  0.014  0.127  0.226  0.087  0.015  0.531\n",
      "LOC0263_SRR6371507  0.646  0.013  0.252  0.041  0.008  0.040\n",
      "LOC0274_SRR6371506  0.035  0.016  0.231  0.210  0.012  0.495\n",
      "LOC0279_SRR6371509  0.028  0.013  0.471  0.169  0.025  0.294\n",
      "LOC0309_SRR6371508  0.174  0.009  0.042  0.020  0.009  0.746\n",
      "LOC0310_SRR6371511  0.009  0.028  0.085  0.192  0.027  0.659\n",
      "LOC0311_SRR6371510  0.019  0.008  0.930  0.025  0.009  0.009}\n",
      "                            0          1\n",
      "LOC0263_SRR6371507  8.000e-04  9.992e-01\n",
      "LOC0040_SRR6371512  1.000e-03  9.990e-01\n",
      "LOC0121_SRR6371520  2.000e-03  9.980e-01\n",
      "LOC0122_SRR6371503  2.700e-03  9.972e-01\n",
      "LOC0127_SRR6371502  1.512e-01  8.487e-01\n",
      "LOC0310_SRR6371511  2.500e-01  7.500e-01\n",
      "LOC0274_SRR6371506  2.507e-01  7.492e-01\n",
      "LOC0035_SRR6371515  2.510e-01  7.490e-01\n",
      "LOC0151_SRR6371505  2.515e-01  7.485e-01\n",
      "LOC0088_SRR6371521  3.583e-01  6.418e-01\n",
      "LOC0309_SRR6371508  3.872e-01  6.128e-01\n",
      "LOC0038_SRR6371513  4.972e-01  5.027e-01\n",
      "LOC0311_SRR6371510  4.992e-01  5.008e-01\n",
      "LOC0037_SRR6371514  4.995e-01  5.005e-01\n",
      "LOC0279_SRR6371509  4.995e-01  5.005e-01\n",
      "LOC0041_SRR6371519  5.835e-01  4.165e-01\n",
      "LOC0051_SRR6371516  9.988e-01  1.300e-03\n",
      "LOC0049_SRR6371518  9.995e-01  5.000e-04\n",
      "LOC0050_SRR6371517  1.000e+00  0.000e+00\n"
     ]
    },
    {
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       "                e.stopPropagation();\n",
       "                e.preventDefault();\n",
       "            }\n",
       "\n",
       "            item.addEventListener(\"mouseover\", mouseover);\n",
       "            item.addEventListener(\"mouseout\", mouseout);\n",
       "            item.addEventListener(\"mouseup\", choose_item);\n",
       "            item.addEventListener(\"contextmenu\", choose_item);\n",
       "\n",
       "            menu.appendChild(item);\n",
       "        };\n",
       "        return module;\n",
       "    })(modules[\"toyplot/root\"],modules[\"toyplot/canvas\"]);\n",
       "modules[\"toyplot/io\"] = (function()\n",
       "    {\n",
       "        var module = {};\n",
       "        module.save_file = function(mime_type, charset, data, filename)\n",
       "        {\n",
       "            var uri = \"data:\" + mime_type + \";charset=\" + charset + \",\" + data;\n",
       "            uri = encodeURI(uri);\n",
       "\n",
       "            var link = document.createElement(\"a\");\n",
       "            if(typeof link.download != \"undefined\")\n",
       "            {\n",
       "              link.href = uri;\n",
       "              link.style = \"visibility:hidden\";\n",
       "              link.download = filename;\n",
       "\n",
       "              document.body.appendChild(link);\n",
       "              link.click();\n",
       "              document.body.removeChild(link);\n",
       "            }\n",
       "            else\n",
       "            {\n",
       "              window.open(uri);\n",
       "            }\n",
       "        };\n",
       "        return module;\n",
       "    })();\n",
       "modules[\"toyplot.coordinates.Axis\"] = (\n",
       "        function(canvas)\n",
       "        {\n",
       "            function sign(x)\n",
       "            {\n",
       "                return x < 0 ? -1 : x > 0 ? 1 : 0;\n",
       "            }\n",
       "\n",
       "            function mix(a, b, amount)\n",
       "            {\n",
       "                return ((1.0 - amount) * a) + (amount * b);\n",
       "            }\n",
       "\n",
       "            function log(x, base)\n",
       "            {\n",
       "                return Math.log(Math.abs(x)) / Math.log(base);\n",
       "            }\n",
       "\n",
       "            function in_range(a, x, b)\n",
       "            {\n",
       "                var left = Math.min(a, b);\n",
       "                var right = Math.max(a, b);\n",
       "                return left <= x && x <= right;\n",
       "            }\n",
       "\n",
       "            function inside(range, projection)\n",
       "            {\n",
       "                for(var i = 0; i != projection.length; ++i)\n",
       "                {\n",
       "                    var segment = projection[i];\n",
       "                    if(in_range(segment.range.min, range, segment.range.max))\n",
       "                        return true;\n",
       "                }\n",
       "                return false;\n",
       "            }\n",
       "\n",
       "            function to_domain(range, projection)\n",
       "            {\n",
       "                for(var i = 0; i != projection.length; ++i)\n",
       "                {\n",
       "                    var segment = projection[i];\n",
       "                    if(in_range(segment.range.bounds.min, range, segment.range.bounds.max))\n",
       "                    {\n",
       "                        if(segment.scale == \"linear\")\n",
       "                        {\n",
       "                            var amount = (range - segment.range.min) / (segment.range.max - segment.range.min);\n",
       "                            return mix(segment.domain.min, segment.domain.max, amount)\n",
       "                        }\n",
       "                        else if(segment.scale[0] == \"log\")\n",
       "                        {\n",
       "                            var amount = (range - segment.range.min) / (segment.range.max - segment.range.min);\n",
       "                            var base = segment.scale[1];\n",
       "                            return sign(segment.domain.min) * Math.pow(base, mix(log(segment.domain.min, base), log(segment.domain.max, base), amount));\n",
       "                        }\n",
       "                    }\n",
       "                }\n",
       "            }\n",
       "\n",
       "            var axes = {};\n",
       "\n",
       "            function display_coordinates(e)\n",
       "            {\n",
       "                var current = canvas.createSVGPoint();\n",
       "                current.x = e.clientX;\n",
       "                current.y = e.clientY;\n",
       "\n",
       "                for(var axis_id in axes)\n",
       "                {\n",
       "                    var axis = document.querySelector(\"#\" + axis_id);\n",
       "                    var coordinates = axis.querySelector(\".toyplot-coordinates-Axis-coordinates\");\n",
       "                    if(coordinates)\n",
       "                    {\n",
       "                        var projection = axes[axis_id];\n",
       "                        var local = current.matrixTransform(axis.getScreenCTM().inverse());\n",
       "                        if(inside(local.x, projection))\n",
       "                        {\n",
       "                            var domain = to_domain(local.x, projection);\n",
       "                            coordinates.style.visibility = \"visible\";\n",
       "                            coordinates.setAttribute(\"transform\", \"translate(\" + local.x + \")\");\n",
       "                            var text = coordinates.querySelector(\"text\");\n",
       "                            text.textContent = domain.toFixed(2);\n",
       "                        }\n",
       "                        else\n",
       "                        {\n",
       "                            coordinates.style.visibility= \"hidden\";\n",
       "                        }\n",
       "                    }\n",
       "                }\n",
       "            }\n",
       "\n",
       "            canvas.addEventListener(\"click\", display_coordinates);\n",
       "\n",
       "            var module = {};\n",
       "            module.show_coordinates = function(axis_id, projection)\n",
       "            {\n",
       "                axes[axis_id] = projection;\n",
       "            }\n",
       "\n",
       "            return module;\n",
       "        })(modules[\"toyplot/canvas\"]);\n",
       "(function(tables, context_menu, io, owner_id, key, label, names, columns, filename)\n",
       "        {\n",
       "            tables.set(owner_id, key, names, columns);\n",
       "\n",
       "            var owner = document.querySelector(\"#\" + owner_id);\n",
       "            function show_item(e)\n",
       "            {\n",
       "                return owner.contains(e.target);\n",
       "            }\n",
       "\n",
       "            function choose_item()\n",
       "            {\n",
       "                io.save_file(\"text/csv\", \"utf-8\", tables.get_csv(owner_id, key), filename + \".csv\");\n",
       "            }\n",
       "\n",
       "            context_menu.add_item(\"Save \" + label + \" as CSV\", show_item, choose_item);\n",
       "        })(modules[\"toyplot/tables\"],modules[\"toyplot/menus/context\"],modules[\"toyplot/io\"],\"t3026fb8e681d4761af0081997e02b24c\",\"data\",\"bar data\",[\"left\", \"right\", \"baseline\", \"magnitude0\", \"magnitude1\"],[[-0.5, 0.5, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5, 11.5, 12.5, 13.5, 14.5, 15.5, 16.5, 17.5], [0.5, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5, 11.5, 12.5, 13.5, 14.5, 15.5, 16.5, 17.5, 18.5], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0008, 0.001, 0.002, 0.0027, 0.1512, 0.25, 0.2507, 0.251, 0.2515, 0.3583, 0.3872, 0.4972, 0.4992, 0.4995, 0.4995, 0.5835, 0.9988, 0.9995, 1.0], [0.9992, 0.999, 0.998, 0.9972, 0.8487, 0.75, 0.7492, 0.749, 0.7485, 0.6418, 0.6128, 0.5027, 0.5008, 0.5005, 0.5005, 0.4165, 0.0013, 0.0005, 0.0]],\"toyplot\");\n",
       "(function(axis, axis_id, projection)\n",
       "        {\n",
       "            axis.show_coordinates(axis_id, projection);\n",
       "        })(modules[\"toyplot.coordinates.Axis\"],\"tf45543f9ff064dba84b8061c9751433a\",[{\"domain\": {\"bounds\": {\"max\": Infinity, \"min\": -Infinity}, \"max\": 1.0001, \"min\": 0.0}, \"range\": {\"bounds\": {\"max\": Infinity, \"min\": -Infinity}, \"max\": 100.0, \"min\": 0.0}, \"scale\": \"linear\"}]);\n",
       "})();</script></div></div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "## set some clumpp params\n",
    "s.clumppparams.m = 3               ## use largegreedy algorithm\n",
    "s.clumppparams.greedy_option = 2   ## test nrepeat possible orders\n",
    "s.clumppparams.repeats = 10000     ## number of repeats\n",
    "s.clumppparams\n",
    "## run clumpp for each value of K\n",
    "#tables = s.get_clumpp_table(kvalues, quiet=True)\n",
    "print(tables)\n",
    "#table = tables[4].sort_values(by=[0, 1, 2, 3])\n",
    "table = tables[2].sort_values(by=[0, 1])\n",
    "toyplot.bars(\n",
    "    table,\n",
    "    width=500, \n",
    "    height=200,\n",
    "    title=[[i] for i in table.index.tolist()],\n",
    "    xshow=False,\n",
    ");\n",
    "print(table)"
   ]
  }
 ],
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