comparison Tryp_V.py @ 8:e75a85590041 draft

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7:25226d33642e

"""
 * Copyright 2018 University of Liverpool
 * Author: John Heap, Computational Biology Facility, UoL
 * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 """

import matplotlib as mpl
mpl.use('Agg')

import subprocess
import shutil
import re
import pandas as pd
import os

import sys

import matplotlib.pyplot as plt
from matplotlib.patches import Patch
import seaborn as sns

def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name):
    #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"
    argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name
    print(argString)
    returncode = subprocess.call(argString, shell=True)
    if returncode != 0:
        return "Error in velveth"
    argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -clean yes -ins_length_sd 50 -min_pair_count 20"
    #argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"
    #argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString
    print(argString)
    returncode = subprocess.call(argString, shell = True)
    if returncode != 0:
        return "Error in velvetg"
    shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa")  # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";
    return "ok"


def blastContigs(test_name,database):
    print(test_name)
    print(database)
    #db_path = os.path.dirname(os.path.realpath(__file__))+database
    db_path = database
    argString = "blastn -db "+db_path+" -query "+test_name+".fa -outfmt 10 -out "+test_name+"_blast.txt"
    print (argString)
    returncode = subprocess.call(argString, shell = True)
    if returncode != 0:
        return "Error in blastall"
    blast_df = pd.read_csv(""+test_name+"_blast.txt")
    #print (blast_df)
    #if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){
    #'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore'
    blast_df.columns = ['qaccver', 'saccver', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue','bitscore']
    blastResult_df = blast_df[(blast_df['pident']>=98) & (blast_df['length'] > 100) & (blast_df['evalue']<0.001) ]
    blastResult_df = blastResult_df[['qaccver', 'saccver', 'pident']]   #query accession.version, subject accession.version, Percentage of identical matches

    return blastResult_df



def getCogsPresent(blastResult_df,strain,cogOrBinList):
    blastResult_df.sort_values('pident',axis = 0, ascending=False, inplace=True)
    nodeList = blastResult_df['qaccver'].tolist()
    cogList = blastResult_df['saccver'].tolist()
    cogSet = set(cogList)   #get unique values
    cogList = sorted(cogSet)    #sort them

    #print (cogList)
    #print (len(cogList))

    thereList = []
    dataList = []
    #dir_path = os.path.dirname(os.path.realpath(__file__))
    fname = cogOrBinList
    cnt = 0
    with open (fname) as f:
        for line in f:
            dataList.append(line.rstrip('\n\r '))
            if line.rstrip('\n\r ') in cogList:
                thereList.append('1')
                cnt = cnt+1
            else:
                thereList.append('0')

    #print (thereList)
    #print (cnt)
    data = {'Cog': dataList, strain: thereList}
    presence_df = pd.DataFrame(data)
    #print (presence_df)
    return presence_df

def addToCurrentData(cog_df, name):
    dir_path = os.path.dirname(os.path.realpath(__file__))
    j_fname = dir_path + r"/data/vivax/TvDatabase.csv"
    tv_df = pd.read_csv(j_fname)

    cogList = cog_df[name].tolist()
    #cogList.insert(0,'Test')
    #print (len(tv_df))
    #print(len(cogList))

    #print(cogList)
    tv_df.loc[:,name]=cogList
    return tv_df




def createClusterMap(tv_df,name,html_path,pdfExport):
    #Retrieve Data
    dir_path = os.path.dirname(os.path.realpath(__file__))
    j_fname = dir_path+r"/data/vivax/geoTv.csv"
    geo_df = pd.read_csv(j_fname)
    geo_df.loc[len(geo_df)] =[name,name,'k']
    print(geo_df)

    myStrains = tv_df.columns.values.tolist()   #beware first entry is COG
    myStrains = myStrains[1:]
    print(myStrains)
    myPal = []
    for s in myStrains:
        col = geo_df[(geo_df['Strain'] == s)]['colour'].tolist()
        myPal.append(col[0])
    print(myPal)
    mycogmap = ['skyblue', 'orangered']  # blue absent,red present
    tv_df.set_index('COG', inplace=True)
    tv_df = tv_df[tv_df.columns].astype(float)

    cg = sns.clustermap(tv_df, method='ward', col_colors=myPal, cmap=mycogmap, yticklabels = 1500, row_cluster=False, linewidths = 0)
    #cg = sns.clustermap(tv_df, method='ward', row_cluster=False, linewidths = 0)
    ax = cg.ax_heatmap
    #xasix ticks and labels.
    ax.xaxis.tick_top()     #set ticks at top
    newlabs = []

    labs = ax.xaxis.get_ticklabels()
    for i in range(0, len(labs)):
        print(labs[i])
        # labs[i].set_text("       "+labs[i].get_text())  #make enough room so label sits atop of col_color bars
        newlabs.append("       " + labs[i].get_text())
    ax.xaxis.set_ticklabels(newlabs)

    #labs = ax.xaxis.get_ticklabels()
    #for i in range(0, len(labs)):
    #    print(labs[i])
    #    labs[i].set_text("       "+labs[i].get_text())  #make enough room so label sits atop of col_color bars
    #    print(labs[i])
    #ax.xaxis.set_ticklabels(labs)
    plt.setp(cg.ax_heatmap.xaxis.get_ticklabels(), rotation=90)  # get x labels printed vertically

    cg.cax.set_visible(False)
    ax = cg.ax_heatmap
    ax.set_yticklabels("")
    ax.set_ylabel("")
    ax = cg.ax_heatmap
    # ax.set_title("Variant antigen profiles of T. vivax genomes.\nDendrogram reflects the VSG repertoire relationships of each strain inferred by the presence and absence of non-universal T. vivax VSG orthologs.", va = "top", wrap = "True")
    b = len(tv_df)
    print(b)
    title = "Figure Legend: The Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ " \
            "showing the \ncombination of present and absent diagnostic cluster of VSG orthologs " \
            "across the sample cohort. \nDendrogram reflects the relationships amongst the VSG" \
            " repertoires of each strain. " \
            "Strains were isolated \nfrom multiple African countries as shown in the key.\nData was produced with the " \
            "'Variant Antigen Profiler' (Silva Pereira and Jackson, 2018)."

    ax.text(-1.5, len(tv_df) + 8,
            title,
            ha="left", va="top", wrap="True")
    col = cg.ax_col_dendrogram.get_position()
    cg.ax_col_dendrogram.set_position([col.x0, col.y0*1.08, col.width, col.height*1.1])

    countryList = pd.unique(geo_df['Location'])
    colourList = pd.unique(geo_df['colour'])
    legend_elements = [Patch(facecolor='orangered', label='COG Present'),
                       Patch(facecolor='skyblue', label='COG Absent')]

    for i in range(0, len(colourList)):
        print("country = %s, colour = %s" % (countryList[i], colourList[i]))
        p = Patch(facecolor=str(colourList[i]), label=countryList[i])
        legend_elements.append(p)

    ax.legend(handles = legend_elements, bbox_to_anchor=(-0.3,1.2),loc = 'upper left')







    #plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0 )  # get y labels printed horizontally
    # cg.dendrogram_col.linkage  # linkage matrix for columns
    # cg.dendrogram_row.linkage  # linkage matrix for rows
    # plt.savefig(r"results/" + name + "_heatmap.png")
    #plt.savefig(htmlresource + "/heatmap.png")
    #if pdf == 'PDF_Yes':
    #    plt.savefig(htmlresource + "/heatmap.pdf")
        # shutil.copyfile("heatmap.pdf",heatmapfn)  #
    #plt.legend()
    fname = html_path+"/"+name+"_clustermap.png"
    cg.savefig(fname)
    if pdfExport == 'PDF_Yes':
        fname = html_path + "/" + name + "_clustermap.pdf"
        cg.savefig(fname)
    #plt.show()

def createHTML(name,htmlfn,htmlPath):
    #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource
    htmlString = r"<html><title>T.vivax VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3>"
    htmlString += name


    htmlString += r'<p> <h3>The Heat Map and Dendrogram</h3></p>'
    imgString = r"<img src = '"+name+"_clustermap.png' alt='Cog Clustermap' style='max-width:100%'><br><br>"
    htmlString += imgString
    print(htmlString)

    with open(htmlfn, "w") as htmlfile:
        htmlfile.write(htmlString)


def vivax_assemble(args,dict):
    #argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10}
    #assembleWithVelvet("V2_Test", '65', '400', '5', "data/TviBrRp.1.clean", "data/TviBrRp.2.clean")

    vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax"
    assembleWithVelvet(args[dict['name']], args[dict['kmers']], args[dict['inslen']], args[dict['covcut']],
                       args[dict['forward']], args[dict['reverse']])
    blastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/COGs.fas")
    orthPresence_df = getCogsPresent(blastResult_df, args[dict['name']], vivaxPath+r"/Database/COGlist.txt")

    binBlastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/Bin_2.fas")
    binPresence_df = getCogsPresent(binBlastResult_df, args[dict['name']], vivaxPath+r"/Database/binlist.txt")
    cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True)

    fname = args[dict['html_resource']] +args[dict['name']]+"_cogspresent.csv"
    cogPresence_df.to_csv(fname)
    current_df = addToCurrentData(cogPresence_df,args[dict['name']])  # load in Tvdatabase and add cogPresence column to it.
    createClusterMap(current_df, args[dict['name']],args[dict['html_resource']],args[dict['pdfexport']])
    createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']])

def test_cluster(args,dict):
    print ("name: %s",args[dict['name']])
    cogPresence_df = pd.read_csv("test_cogspresent.csv")
    print(cogPresence_df)
    current_df = addToCurrentData(cogPresence_df,args[dict['name']])  # load in Tvdatabase and add cogPresence column to it.
    createClusterMap(current_df, args[dict['name']], args[dict['html_resource']], args[dict['pdfexport']])

def vivax_contigs(args,dict):
# argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6}

    #test_cluster(args,dict)
    #return;

    #subprocess.call('echo $PATH',shell = True)
    #sys.exit(1)

    vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax"
    shutil.copyfile(args[dict['contigs']], args[dict['name']]+".fa")
    blastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/COGs.fas")
    orthPresence_df = getCogsPresent(blastResult_df, args[dict['name']], vivaxPath+r"/Database/COGlist.txt")

    binBlastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/Bin_2.fas")
    binPresence_df = getCogsPresent(binBlastResult_df, args[dict['name']], vivaxPath+r"/Database/binlist.txt")
    cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True)

    fname = args[dict['html_resource']]+r"/"+ args[dict['name']]+"_cogspresent.csv"
    cogPresence_df.to_csv(fname)
    current_df = addToCurrentData(cogPresence_df,args[dict['name']])  # load in Tvdatabase and add cogPresence column to it.
    createClusterMap(current_df, args[dict['name']], args[dict['html_resource']], args[dict['pdfexport']])
    createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']])

if __name__ == "__main__":
    #assembleWithVelvet("V2_Test",'65','400', '5',"data/TviBrRp.1.clean","data/TviBrRp.2.clean")
    #assembleWithVelvet("V2_Test",'65','400', '5',"data/Tv493.1","data/Tv493.2")
    #blastResult_df=blastContigs("V2_Test",r"/Database/COGs.fas")
    cogPresence_df = pd.read_csv("test_cogspresent.csv")
    print(cogPresence_df)
    current_df = addToCurrentData(cogPresence_df,"vTest")  # load in Tvdatabase and add cogPresence column to it.
    createClusterMap(current_df, "vTest", "sausages","no")
    createHTML("vTest","vTest.html","sausages")
    sys.exit()

    blastResult_df=blastContigs("Tv493",r"/Database/COGs.fas")
    orthPresence_df = getCogsPresent(blastResult_df,"Tv493",r"/Database/COGlist.txt")

    #binBlastResult_df=blastContigs("V2_Test",r"/Database/Bin_2.fas")

    binBlastResult_df=blastContigs("Tv493",r"/Database/Bin_2.fas")
    binPresence_df = getCogsPresent(binBlastResult_df,"Tv493",r"/Database/binlist.txt")
    cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True)
    #now do the next bit?
    current_df = addToCurrentData(cogPresence_df)  # load in Tvdatabase and add cogPresence column to it.
    createClusterMap(current_df,'Test',dict['html_resource'] ,dict['pdfexport'])


    #print(cogPresence_df)
    dir_path = os.path.dirname(os.path.realpath(__file__))
    fname = dir_path+r"/results/V2_TestPresence.csv"
    #fnameb = dir_path+r"/results/V2_Test_blastOrth.csv"
    #fnameb_bin = dir_path+r"/results/V2_Test_blastBin.csv"
    #binBlastResult_df.to_csv(fnameb_bin)
    #blastResult_df.to_csv(fnameb)

    #cogPresence_df.to_csv(fname)
    cogPresence_df = pd.read_csv(fname)

    current_df = addToCurrentData(cogPresence_df)       #load in Tvdatabase and add cogPresence column to it.

8:e75a85590041

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        <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">&quot;&quot;&quot;</span></span></td>
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        <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
        <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib <span class="pl-k">as</span> mpl</td>
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        <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
        <td id="LC21" class="blob-code blob-code-inner js-file-line">mpl.use(<span class="pl-s"><span class="pl-pds">&#39;</span>Agg<span class="pl-pds">&#39;</span></span>)</td>
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</td>
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        <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
        <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td>
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        <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td>
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        <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
        <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td>
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      <tr>
        <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
        <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td>
      </tr>
      <tr>
        <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
        <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td>
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        <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
        <td id="LC28" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
        <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
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      <tr>
        <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
        <td id="LC30" class="blob-code blob-code-inner js-file-line">
</td>
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      <tr>
        <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
        <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td>
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      <tr>
        <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
        <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">from</span> matplotlib.patches <span class="pl-k">import</span> Patch</td>
      </tr>
      <tr>
        <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
        <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> seaborn <span class="pl-k">as</span> sns</td>
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      <tr>
        <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
        <td id="LC34" class="blob-code blob-code-inner js-file-line">
</td>
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      <tr>
        <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
        <td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">assembleWithVelvet</span>(<span class="pl-smi">name</span>, <span class="pl-smi">kmers</span>, <span class="pl-smi">inslen</span>, <span class="pl-smi">covcut</span>, <span class="pl-smi">fastq1name</span>,<span class="pl-smi">fastq2name</span>):</td>
      </tr>
      <tr>
        <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
        <td id="LC36" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>argString = &quot;velveth &quot; + name + &quot;_k65 65 -shortPaired -fastq &quot; + name + &quot;_R1.fastq &quot; + name + &quot;_R2.fastq&quot;</span></td>
      </tr>
      <tr>
        <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
        <td id="LC37" class="blob-code blob-code-inner js-file-line">    argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>velveth <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> kmers <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span> -shortPaired -fastq <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> fastq1name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>fastq2name</td>
      </tr>
      <tr>
        <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
        <td id="LC38" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(argString)</td>
      </tr>
      <tr>
        <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
        <td id="LC39" class="blob-code blob-code-inner js-file-line">    returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
      </tr>
      <tr>
        <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
        <td id="LC40" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
      </tr>
      <tr>
        <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
        <td id="LC41" class="blob-code blob-code-inner js-file-line">        <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Error in velveth<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
        <td id="LC42" class="blob-code blob-code-inner js-file-line">    argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>velvetg <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -exp_cov auto -ins_length <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inslen<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -clean yes -ins_length_sd 50 -min_pair_count 20<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
        <td id="LC43" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>argString = &quot;velvetg &quot; + name + &quot;_k&quot;+kmers+&quot; -exp_cov auto -ins_length &quot;+inslen+&quot; -cov_cutoff &quot;+covcut+&quot; -clean yes -ins_length_sd 50 -min_pair_count 20&quot;</span></td>
      </tr>
      <tr>
        <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
        <td id="LC44" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>argString = &quot;velvetg &quot; + name + &quot;_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20&quot;+quietString</span></td>
      </tr>
      <tr>
        <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
        <td id="LC45" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(argString)</td>
      </tr>
      <tr>
        <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
        <td id="LC46" class="blob-code blob-code-inner js-file-line">    returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td>
      </tr>
      <tr>
        <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
        <td id="LC47" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
      </tr>
      <tr>
        <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
        <td id="LC48" class="blob-code blob-code-inner js-file-line">        <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Error in velvetg<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
        <td id="LC49" class="blob-code blob-code-inner js-file-line">    shutil.copyfile(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>//contigs.fa<span class="pl-pds">&quot;</span></span>,name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.fa<span class="pl-pds">&quot;</span></span>)  <span class="pl-c"><span class="pl-c">#</span> my $namechange = &quot;mv &quot;.$input.&quot;_k65/contigs.fa &quot;.$input.&quot;.fa&quot;;</span></td>
      </tr>
      <tr>
        <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
        <td id="LC50" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ok<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
        <td id="LC51" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
        <td id="LC52" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
        <td id="LC53" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">database</span>):</td>
      </tr>
      <tr>
        <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
        <td id="LC54" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(test_name)</td>
      </tr>
      <tr>
        <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
        <td id="LC55" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(database)</td>
      </tr>
      <tr>
        <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
        <td id="LC56" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>db_path = os.path.dirname(os.path.realpath(__file__))+database</span></td>
      </tr>
      <tr>
        <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
        <td id="LC57" class="blob-code blob-code-inner js-file-line">    db_path <span class="pl-k">=</span> database</td>
      </tr>
      <tr>
        <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
        <td id="LC58" class="blob-code blob-code-inner js-file-line">    argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>blastn -db <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -query <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.fa -outfmt 10 -out <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_blast.txt<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
        <td id="LC59" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(argString)</td>
      </tr>
      <tr>
        <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
        <td id="LC60" class="blob-code blob-code-inner js-file-line">    returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td>
      </tr>
      <tr>
        <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
        <td id="LC61" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td>
      </tr>
      <tr>
        <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
        <td id="LC62" class="blob-code blob-code-inner js-file-line">        <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Error in blastall<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
        <td id="LC63" class="blob-code blob-code-inner js-file-line">    blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_blast.txt<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
        <td id="LC64" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print (blast_df)</span></td>
      </tr>
      <tr>
        <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
        <td id="LC65" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>if ($temp[2] &gt;= 98 &amp; &amp; $temp[3] &gt; 100 &amp; &amp; $temp[10] &lt; 0.001){</span></td>
      </tr>
      <tr>
        <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
        <td id="LC66" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>&#39;qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore&#39;</span></td>
      </tr>
      <tr>
        <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
        <td id="LC67" class="blob-code blob-code-inner js-file-line">    blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>length<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>mismatch<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>gapopen<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>qstart<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>qend<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>sstart<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>send<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>bitscore<span class="pl-pds">&#39;</span></span>]</td>
      </tr>
      <tr>
        <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
        <td id="LC68" class="blob-code blob-code-inner js-file-line">    blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>]<span class="pl-k">&gt;=</span><span class="pl-c1">98</span>) <span class="pl-k">&amp;</span> (blast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>length<span class="pl-pds">&#39;</span></span>] <span class="pl-k">&gt;</span> <span class="pl-c1">100</span>) <span class="pl-k">&amp;</span> (blast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>]<span class="pl-k">&lt;</span><span class="pl-c1">0.001</span>) ]</td>
      </tr>
      <tr>
        <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
        <td id="LC69" class="blob-code blob-code-inner js-file-line">    blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>]]   <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td>
      </tr>
      <tr>
        <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
        <td id="LC70" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
        <td id="LC71" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">return</span> blastResult_df</td>
      </tr>
      <tr>
        <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
        <td id="LC72" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
        <td id="LC73" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
        <td id="LC74" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
        <td id="LC75" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getCogsPresent</span>(<span class="pl-smi">blastResult_df</span>,<span class="pl-smi">strain</span>,<span class="pl-smi">cogOrBinList</span>):</td>
      </tr>
      <tr>
        <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
        <td id="LC76" class="blob-code blob-code-inner js-file-line">    blastResult_df.sort_values(<span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>,<span class="pl-v">axis</span> <span class="pl-k">=</span> <span class="pl-c1">0</span>, <span class="pl-v">ascending</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
      </tr>
      <tr>
        <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
        <td id="LC77" class="blob-code blob-code-inner js-file-line">    nodeList <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>].tolist()</td>
      </tr>
      <tr>
        <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
        <td id="LC78" class="blob-code blob-code-inner js-file-line">    cogList <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>].tolist()</td>
      </tr>
      <tr>
        <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
        <td id="LC79" class="blob-code blob-code-inner js-file-line">    cogSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(cogList)   <span class="pl-c"><span class="pl-c">#</span>get unique values</span></td>
      </tr>
      <tr>
        <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
        <td id="LC80" class="blob-code blob-code-inner js-file-line">    cogList <span class="pl-k">=</span> <span class="pl-c1">sorted</span>(cogSet)    <span class="pl-c"><span class="pl-c">#</span>sort them</span></td>
      </tr>
      <tr>
        <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
        <td id="LC81" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
        <td id="LC82" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print (cogList)</span></td>
      </tr>
      <tr>
        <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
        <td id="LC83" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print (len(cogList))</span></td>
      </tr>
      <tr>
        <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
        <td id="LC84" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
        <td id="LC85" class="blob-code blob-code-inner js-file-line">    thereList <span class="pl-k">=</span> []</td>
      </tr>
      <tr>
        <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
        <td id="LC86" class="blob-code blob-code-inner js-file-line">    dataList <span class="pl-k">=</span> []</td>
      </tr>
      <tr>
        <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
        <td id="LC87" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>dir_path = os.path.dirname(os.path.realpath(__file__))</span></td>
      </tr>
      <tr>
        <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
        <td id="LC88" class="blob-code blob-code-inner js-file-line">    fname <span class="pl-k">=</span> cogOrBinList</td>
      </tr>
      <tr>
        <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
        <td id="LC89" class="blob-code blob-code-inner js-file-line">    cnt <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
      </tr>
      <tr>
        <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
        <td id="LC90" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">with</span> <span class="pl-c1">open</span> (fname) <span class="pl-k">as</span> f:</td>
      </tr>
      <tr>
        <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
        <td id="LC91" class="blob-code blob-code-inner js-file-line">        <span class="pl-k">for</span> line <span class="pl-k">in</span> f:</td>
      </tr>
      <tr>
        <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
        <td id="LC92" class="blob-code blob-code-inner js-file-line">            dataList.append(line.rstrip(<span class="pl-s"><span class="pl-pds">&#39;</span><span class="pl-cce">\n\r</span> <span class="pl-pds">&#39;</span></span>))</td>
      </tr>
      <tr>
        <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
        <td id="LC93" class="blob-code blob-code-inner js-file-line">            <span class="pl-k">if</span> line.rstrip(<span class="pl-s"><span class="pl-pds">&#39;</span><span class="pl-cce">\n\r</span> <span class="pl-pds">&#39;</span></span>) <span class="pl-k">in</span> cogList:</td>
      </tr>
      <tr>
        <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
        <td id="LC94" class="blob-code blob-code-inner js-file-line">                thereList.append(<span class="pl-s"><span class="pl-pds">&#39;</span>1<span class="pl-pds">&#39;</span></span>)</td>
      </tr>
      <tr>
        <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
        <td id="LC95" class="blob-code blob-code-inner js-file-line">                cnt <span class="pl-k">=</span> cnt<span class="pl-k">+</span><span class="pl-c1">1</span></td>
      </tr>
      <tr>
        <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
        <td id="LC96" class="blob-code blob-code-inner js-file-line">            <span class="pl-k">else</span>:</td>
      </tr>
      <tr>
        <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
        <td id="LC97" class="blob-code blob-code-inner js-file-line">                thereList.append(<span class="pl-s"><span class="pl-pds">&#39;</span>0<span class="pl-pds">&#39;</span></span>)</td>
      </tr>
      <tr>
        <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
        <td id="LC98" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
        <td id="LC99" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print (thereList)</span></td>
      </tr>
      <tr>
        <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
        <td id="LC100" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print (cnt)</span></td>
      </tr>
      <tr>
        <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
        <td id="LC101" class="blob-code blob-code-inner js-file-line">    data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>Cog<span class="pl-pds">&#39;</span></span>: dataList, strain: thereList}</td>
      </tr>
      <tr>
        <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
        <td id="LC102" class="blob-code blob-code-inner js-file-line">    presence_df <span class="pl-k">=</span> pd.DataFrame(data)</td>
      </tr>
      <tr>
        <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
        <td id="LC103" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print (presence_df)</span></td>
      </tr>
      <tr>
        <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
        <td id="LC104" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">return</span> presence_df</td>
      </tr>
      <tr>
        <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
        <td id="LC105" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
        <td id="LC106" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">addToCurrentData</span>(<span class="pl-smi">cog_df</span>, <span class="pl-smi">name</span>):</td>
      </tr>
      <tr>
        <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
        <td id="LC107" class="blob-code blob-code-inner js-file-line">    dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
      </tr>
      <tr>
        <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
        <td id="LC108" class="blob-code blob-code-inner js-file-line">    j_fname <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/data/vivax/TvDatabase<span class="pl-c1">.</span>csv<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
        <td id="LC109" class="blob-code blob-code-inner js-file-line">    tv_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
      </tr>
      <tr>
        <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
        <td id="LC110" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
        <td id="LC111" class="blob-code blob-code-inner js-file-line">    cogList <span class="pl-k">=</span> cog_df[name].tolist()</td>
      </tr>
      <tr>
        <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
        <td id="LC112" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>cogList.insert(0,&#39;Test&#39;)</span></td>
      </tr>
      <tr>
        <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
        <td id="LC113" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print (len(tv_df))</span></td>
      </tr>
      <tr>
        <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
        <td id="LC114" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print(len(cogList))</span></td>
      </tr>
      <tr>
        <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
        <td id="LC115" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
        <td id="LC116" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print(cogList)</span></td>
      </tr>
      <tr>
        <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
        <td id="LC117" class="blob-code blob-code-inner js-file-line">    tv_df.loc[:,name]<span class="pl-k">=</span>cogList</td>
      </tr>
      <tr>
        <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
        <td id="LC118" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">return</span> tv_df</td>
      </tr>
      <tr>
        <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
        <td id="LC119" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
        <td id="LC120" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
        <td id="LC121" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
        <td id="LC122" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
        <td id="LC123" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createClusterMap</span>(<span class="pl-smi">tv_df</span>,<span class="pl-smi">name</span>,<span class="pl-smi">html_path</span>,<span class="pl-smi">pdfExport</span>):</td>
      </tr>
      <tr>
        <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
        <td id="LC124" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>Retrieve Data</span></td>
      </tr>
      <tr>
        <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
        <td id="LC125" class="blob-code blob-code-inner js-file-line">    dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
      </tr>
      <tr>
        <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
        <td id="LC126" class="blob-code blob-code-inner js-file-line">    j_fname <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/data/vivax/geoTv<span class="pl-c1">.</span>csv<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
        <td id="LC127" class="blob-code blob-code-inner js-file-line">    geo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td>
      </tr>
      <tr>
        <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
        <td id="LC128" class="blob-code blob-code-inner js-file-line">    geo_df.loc[<span class="pl-c1">len</span>(geo_df)] <span class="pl-k">=</span>[name,name,<span class="pl-s"><span class="pl-pds">&#39;</span>k<span class="pl-pds">&#39;</span></span>]</td>
      </tr>
      <tr>
        <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
        <td id="LC129" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(geo_df)</td>
      </tr>
      <tr>
        <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
        <td id="LC130" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
        <td id="LC131" class="blob-code blob-code-inner js-file-line">    myStrains <span class="pl-k">=</span> tv_df.columns.values.tolist()   <span class="pl-c"><span class="pl-c">#</span>beware first entry is COG</span></td>
      </tr>
      <tr>
        <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
        <td id="LC132" class="blob-code blob-code-inner js-file-line">    myStrains <span class="pl-k">=</span> myStrains[<span class="pl-c1">1</span>:]</td>
      </tr>
      <tr>
        <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
        <td id="LC133" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(myStrains)</td>
      </tr>
      <tr>
        <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
        <td id="LC134" class="blob-code blob-code-inner js-file-line">    myPal <span class="pl-k">=</span> []</td>
      </tr>
      <tr>
        <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
        <td id="LC135" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">for</span> s <span class="pl-k">in</span> myStrains:</td>
      </tr>
      <tr>
        <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
        <td id="LC136" class="blob-code blob-code-inner js-file-line">        col <span class="pl-k">=</span> geo_df[(geo_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Strain<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> s)][<span class="pl-s"><span class="pl-pds">&#39;</span>colour<span class="pl-pds">&#39;</span></span>].tolist()</td>
      </tr>
      <tr>
        <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
        <td id="LC137" class="blob-code blob-code-inner js-file-line">        myPal.append(col[<span class="pl-c1">0</span>])</td>
      </tr>
      <tr>
        <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
        <td id="LC138" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(myPal)</td>
      </tr>
      <tr>
        <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
        <td id="LC139" class="blob-code blob-code-inner js-file-line">    mycogmap <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>skyblue<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>orangered<span class="pl-pds">&#39;</span></span>]  <span class="pl-c"><span class="pl-c">#</span> blue absent,red present</span></td>
      </tr>
      <tr>
        <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
        <td id="LC140" class="blob-code blob-code-inner js-file-line">    tv_df.set_index(<span class="pl-s"><span class="pl-pds">&#39;</span>COG<span class="pl-pds">&#39;</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
      </tr>
      <tr>
        <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
        <td id="LC141" class="blob-code blob-code-inner js-file-line">    tv_df <span class="pl-k">=</span> tv_df[tv_df.columns].astype(<span class="pl-c1">float</span>)</td>
      </tr>
      <tr>
        <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
        <td id="LC142" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
        <td id="LC143" class="blob-code blob-code-inner js-file-line">    cg <span class="pl-k">=</span> sns.clustermap(tv_df, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>ward<span class="pl-pds">&#39;</span></span>, <span class="pl-v">col_colors</span><span class="pl-k">=</span>myPal, <span class="pl-v">cmap</span><span class="pl-k">=</span>mycogmap, <span class="pl-v">yticklabels</span> <span class="pl-k">=</span> <span class="pl-c1">1500</span>, <span class="pl-v">row_cluster</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">linewidths</span> <span class="pl-k">=</span> <span class="pl-c1">0</span>)</td>
      </tr>
      <tr>
        <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
        <td id="LC144" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>cg = sns.clustermap(tv_df, method=&#39;ward&#39;, row_cluster=False, linewidths = 0)</span></td>
      </tr>
      <tr>
        <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
        <td id="LC145" class="blob-code blob-code-inner js-file-line">    ax <span class="pl-k">=</span> cg.ax_heatmap</td>
      </tr>
      <tr>
        <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
        <td id="LC146" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>xasix ticks and labels.</span></td>
      </tr>
      <tr>
        <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
        <td id="LC147" class="blob-code blob-code-inner js-file-line">    ax.xaxis.tick_top()     <span class="pl-c"><span class="pl-c">#</span>set ticks at top</span></td>
      </tr>
      <tr>
        <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
        <td id="LC148" class="blob-code blob-code-inner js-file-line">    newlabs <span class="pl-k">=</span> []</td>
      </tr>
      <tr>
        <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
        <td id="LC149" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
        <td id="LC150" class="blob-code blob-code-inner js-file-line">    labs <span class="pl-k">=</span> ax.xaxis.get_ticklabels()</td>
      </tr>
      <tr>
        <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
        <td id="LC151" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(labs)):</td>
      </tr>
      <tr>
        <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
        <td id="LC152" class="blob-code blob-code-inner js-file-line">        <span class="pl-c1">print</span>(labs[i])</td>
      </tr>
      <tr>
        <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
        <td id="LC153" class="blob-code blob-code-inner js-file-line">        <span class="pl-c"><span class="pl-c">#</span> labs[i].set_text(&quot;       &quot;+labs[i].get_text())  #make enough room so label sits atop of col_color bars</span></td>
      </tr>
      <tr>
        <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
        <td id="LC154" class="blob-code blob-code-inner js-file-line">        newlabs.append(<span class="pl-s"><span class="pl-pds">&quot;</span>       <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> labs[i].get_text())</td>
      </tr>
      <tr>
        <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
        <td id="LC155" class="blob-code blob-code-inner js-file-line">    ax.xaxis.set_ticklabels(newlabs)</td>
      </tr>
      <tr>
        <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
        <td id="LC156" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
        <td id="LC157" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>labs = ax.xaxis.get_ticklabels()</span></td>
      </tr>
      <tr>
        <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
        <td id="LC158" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>for i in range(0, len(labs)):</span></td>
      </tr>
      <tr>
        <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
        <td id="LC159" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>    print(labs[i])</span></td>
      </tr>
      <tr>
        <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
        <td id="LC160" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>    labs[i].set_text(&quot;       &quot;+labs[i].get_text())  #make enough room so label sits atop of col_color bars</span></td>
      </tr>
      <tr>
        <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
        <td id="LC161" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>    print(labs[i])</span></td>
      </tr>
      <tr>
        <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
        <td id="LC162" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>ax.xaxis.set_ticklabels(labs)</span></td>
      </tr>
      <tr>
        <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
        <td id="LC163" class="blob-code blob-code-inner js-file-line">    plt.setp(cg.ax_heatmap.xaxis.get_ticklabels(), <span class="pl-v">rotation</span><span class="pl-k">=</span><span class="pl-c1">90</span>)  <span class="pl-c"><span class="pl-c">#</span> get x labels printed vertically</span></td>
      </tr>
      <tr>
        <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
        <td id="LC164" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
        <td id="LC165" class="blob-code blob-code-inner js-file-line">    cg.cax.set_visible(<span class="pl-c1">False</span>)</td>
      </tr>
      <tr>
        <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
        <td id="LC166" class="blob-code blob-code-inner js-file-line">    ax <span class="pl-k">=</span> cg.ax_heatmap</td>
      </tr>
      <tr>
        <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
        <td id="LC167" class="blob-code blob-code-inner js-file-line">    ax.set_yticklabels(<span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
        <td id="LC168" class="blob-code blob-code-inner js-file-line">    ax.set_ylabel(<span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
        <td id="LC169" class="blob-code blob-code-inner js-file-line">    ax <span class="pl-k">=</span> cg.ax_heatmap</td>
      </tr>
      <tr>
        <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
        <td id="LC170" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span> ax.set_title(&quot;Variant antigen profiles of T. vivax genomes.\nDendrogram reflects the VSG repertoire relationships of each strain inferred by the presence and absence of non-universal T. vivax VSG orthologs.&quot;, va = &quot;top&quot;, wrap = &quot;True&quot;)</span></td>
      </tr>
      <tr>
        <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
        <td id="LC171" class="blob-code blob-code-inner js-file-line">    b <span class="pl-k">=</span> <span class="pl-c1">len</span>(tv_df)</td>
      </tr>
      <tr>
        <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
        <td id="LC172" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(b)</td>
      </tr>
      <tr>
        <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
        <td id="LC173" class="blob-code blob-code-inner js-file-line">    title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Figure Legend: The Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ <span class="pl-pds">&quot;</span></span> \</td>
      </tr>
      <tr>
        <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
        <td id="LC174" class="blob-code blob-code-inner js-file-line">            <span class="pl-s"><span class="pl-pds">&quot;</span>showing the <span class="pl-cce">\n</span>combination of present and absent diagnostic cluster of VSG orthologs <span class="pl-pds">&quot;</span></span> \</td>
      </tr>
      <tr>
        <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
        <td id="LC175" class="blob-code blob-code-inner js-file-line">            <span class="pl-s"><span class="pl-pds">&quot;</span>across the sample cohort. <span class="pl-cce">\n</span>Dendrogram reflects the relationships amongst the VSG<span class="pl-pds">&quot;</span></span> \</td>
      </tr>
      <tr>
        <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
        <td id="LC176" class="blob-code blob-code-inner js-file-line">            <span class="pl-s"><span class="pl-pds">&quot;</span> repertoires of each strain. <span class="pl-pds">&quot;</span></span> \</td>
      </tr>
      <tr>
        <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
        <td id="LC177" class="blob-code blob-code-inner js-file-line">            <span class="pl-s"><span class="pl-pds">&quot;</span>Strains were isolated <span class="pl-cce">\n</span>from multiple African countries as shown in the key.<span class="pl-cce">\n</span>Data was produced with the <span class="pl-pds">&quot;</span></span> \</td>
      </tr>
      <tr>
        <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
        <td id="LC178" class="blob-code blob-code-inner js-file-line">            <span class="pl-s"><span class="pl-pds">&quot;</span>&#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
        <td id="LC179" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
        <td id="LC180" class="blob-code blob-code-inner js-file-line">    ax.text(<span class="pl-k">-</span><span class="pl-c1">1.5</span>, <span class="pl-c1">len</span>(tv_df) <span class="pl-k">+</span> <span class="pl-c1">8</span>,</td>
      </tr>
      <tr>
        <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
        <td id="LC181" class="blob-code blob-code-inner js-file-line">            title,</td>
      </tr>
      <tr>
        <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
        <td id="LC182" class="blob-code blob-code-inner js-file-line">            <span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>left<span class="pl-pds">&quot;</span></span>, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>top<span class="pl-pds">&quot;</span></span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>True<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
        <td id="LC183" class="blob-code blob-code-inner js-file-line">    col <span class="pl-k">=</span> cg.ax_col_dendrogram.get_position()</td>
      </tr>
      <tr>
        <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
        <td id="LC184" class="blob-code blob-code-inner js-file-line">    cg.ax_col_dendrogram.set_position([col.x0, col.y0<span class="pl-k">*</span><span class="pl-c1">1.08</span>, col.width, col.height<span class="pl-k">*</span><span class="pl-c1">1.1</span>])</td>
      </tr>
      <tr>
        <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
        <td id="LC185" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
        <td id="LC186" class="blob-code blob-code-inner js-file-line">    countryList <span class="pl-k">=</span> pd.unique(geo_df[<span class="pl-s"><span class="pl-pds">&#39;</span>Location<span class="pl-pds">&#39;</span></span>])</td>
      </tr>
      <tr>
        <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
        <td id="LC187" class="blob-code blob-code-inner js-file-line">    colourList <span class="pl-k">=</span> pd.unique(geo_df[<span class="pl-s"><span class="pl-pds">&#39;</span>colour<span class="pl-pds">&#39;</span></span>])</td>
      </tr>
      <tr>
        <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
        <td id="LC188" class="blob-code blob-code-inner js-file-line">    legend_elements <span class="pl-k">=</span> [Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>orangered<span class="pl-pds">&#39;</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>COG Present<span class="pl-pds">&#39;</span></span>),</td>
      </tr>
      <tr>
        <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
        <td id="LC189" class="blob-code blob-code-inner js-file-line">                       Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>skyblue<span class="pl-pds">&#39;</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>COG Absent<span class="pl-pds">&#39;</span></span>)]</td>
      </tr>
      <tr>
        <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
        <td id="LC190" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
        <td id="LC191" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(colourList)):</td>
      </tr>
      <tr>
        <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
        <td id="LC192" class="blob-code blob-code-inner js-file-line">        <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>country = <span class="pl-c1">%s</span>, colour = <span class="pl-c1">%s</span><span class="pl-pds">&quot;</span></span> <span class="pl-k">%</span> (countryList[i], colourList[i]))</td>
      </tr>
      <tr>
        <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
        <td id="LC193" class="blob-code blob-code-inner js-file-line">        p <span class="pl-k">=</span> Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-c1">str</span>(colourList[i]), <span class="pl-v">label</span><span class="pl-k">=</span>countryList[i])</td>
      </tr>
      <tr>
        <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
        <td id="LC194" class="blob-code blob-code-inner js-file-line">        legend_elements.append(p)</td>
      </tr>
      <tr>
        <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
        <td id="LC195" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
        <td id="LC196" class="blob-code blob-code-inner js-file-line">    ax.legend(<span class="pl-v">handles</span> <span class="pl-k">=</span> legend_elements, <span class="pl-v">bbox_to_anchor</span><span class="pl-k">=</span>(<span class="pl-k">-</span><span class="pl-c1">0.3</span>,<span class="pl-c1">1.2</span>),<span class="pl-v">loc</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&#39;</span>upper left<span class="pl-pds">&#39;</span></span>)</td>
      </tr>
      <tr>
        <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
        <td id="LC197" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
        <td id="LC198" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
        <td id="LC199" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
        <td id="LC200" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
        <td id="LC201" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
        <td id="LC202" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
        <td id="LC203" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
        <td id="LC204" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0 )  # get y labels printed horizontally</span></td>
      </tr>
      <tr>
        <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
        <td id="LC205" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_col.linkage  # linkage matrix for columns</span></td>
      </tr>
      <tr>
        <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
        <td id="LC206" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_row.linkage  # linkage matrix for rows</span></td>
      </tr>
      <tr>
        <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
        <td id="LC207" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span> plt.savefig(r&quot;results/&quot; + name + &quot;_heatmap.png&quot;)</span></td>
      </tr>
      <tr>
        <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
        <td id="LC208" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>plt.savefig(htmlresource + &quot;/heatmap.png&quot;)</span></td>
      </tr>
      <tr>
        <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
        <td id="LC209" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>if pdf == &#39;PDF_Yes&#39;:</span></td>
      </tr>
      <tr>
        <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
        <td id="LC210" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>    plt.savefig(htmlresource + &quot;/heatmap.pdf&quot;)</span></td>
      </tr>
      <tr>
        <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
        <td id="LC211" class="blob-code blob-code-inner js-file-line">        <span class="pl-c"><span class="pl-c">#</span> shutil.copyfile(&quot;heatmap.pdf&quot;,heatmapfn)  #</span></td>
      </tr>
      <tr>
        <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
        <td id="LC212" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>plt.legend()</span></td>
      </tr>
      <tr>
        <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
        <td id="LC213" class="blob-code blob-code-inner js-file-line">    fname <span class="pl-k">=</span> html_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_clustermap.png<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
        <td id="LC214" class="blob-code blob-code-inner js-file-line">    cg.savefig(fname)</td>
      </tr>
      <tr>
        <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
        <td id="LC215" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">if</span> pdfExport <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>:</td>
      </tr>
      <tr>
        <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
        <td id="LC216" class="blob-code blob-code-inner js-file-line">        fname <span class="pl-k">=</span> html_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_clustermap.pdf<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
        <td id="LC217" class="blob-code blob-code-inner js-file-line">        cg.savefig(fname)</td>
      </tr>
      <tr>
        <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
        <td id="LC218" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
      </tr>
      <tr>
        <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
        <td id="LC219" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
        <td id="LC220" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">name</span>,<span class="pl-smi">htmlfn</span>,<span class="pl-smi">htmlPath</span>):</td>
      </tr>
      <tr>
        <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
        <td id="LC221" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
      </tr>
      <tr>
        <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
        <td id="LC222" class="blob-code blob-code-inner js-file-line">    htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;html&gt;&lt;title&gt;T<span class="pl-c1">.</span>vivax VAP&lt;/title&gt;&lt;body&gt;&lt;div style=&#39;text-align:center&#39;&gt;&lt;h2&gt;&lt;i&gt;Trypanosoma vivax&lt;/i&gt; Variant Antigen Profile&lt;/h2&gt;&lt;h3&gt;<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
        <td id="LC223" class="blob-code blob-code-inner js-file-line">    htmlString <span class="pl-k">+=</span> name</td>
      </tr>
      <tr>
        <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
        <td id="LC224" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
        <td id="LC225" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
        <td id="LC226" class="blob-code blob-code-inner js-file-line">    htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&#39;</span>&lt;p&gt; &lt;h3&gt;The Heat Map and Dendrogram&lt;/h3&gt;&lt;/p&gt;<span class="pl-pds">&#39;</span></span></td>
      </tr>
      <tr>
        <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
        <td id="LC227" class="blob-code blob-code-inner js-file-line">    imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;img src = &#39;<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_clustermap.png&#39; alt=&#39;Cog Clustermap&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
        <td id="LC228" class="blob-code blob-code-inner js-file-line">    htmlString <span class="pl-k">+=</span> imgString</td>
      </tr>
      <tr>
        <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
        <td id="LC229" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(htmlString)</td>
      </tr>
      <tr>
        <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
        <td id="LC230" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
        <td id="LC231" class="blob-code blob-code-inner js-file-line">    <span class="pl-k">with</span> <span class="pl-c1">open</span>(htmlfn, <span class="pl-s"><span class="pl-pds">&quot;</span>w<span class="pl-pds">&quot;</span></span>) <span class="pl-k">as</span> htmlfile:</td>
      </tr>
      <tr>
        <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
        <td id="LC232" class="blob-code blob-code-inner js-file-line">        htmlfile.write(htmlString)</td>
      </tr>
      <tr>
        <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
        <td id="LC233" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
        <td id="LC234" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
        <td id="LC235" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">vivax_assemble</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
      </tr>
      <tr>
        <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
        <td id="LC236" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>argdict = {&#39;name&#39;: 2, &#39;pdfexport&#39;: 3, &#39;kmers&#39;: 4, &#39;inslen&#39;: 5, &#39;covcut&#39;: 6, &#39;forward&#39;: 7, &#39;reverse&#39;: 8, &#39;html_file&#39;: 9,&#39;html_resource&#39;: 10}</span></td>
      </tr>
      <tr>
        <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
        <td id="LC237" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>assembleWithVelvet(&quot;V2_Test&quot;, &#39;65&#39;, &#39;400&#39;, &#39;5&#39;, &quot;data/TviBrRp.1.clean&quot;, &quot;data/TviBrRp.2.clean&quot;)</span></td>
      </tr>
      <tr>
        <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
        <td id="LC238" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
        <td id="LC239" class="blob-code blob-code-inner js-file-line">    vivaxPath <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/data/vivax<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
        <td id="LC240" class="blob-code blob-code-inner js-file-line">    assembleWithVelvet(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>kmers<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>inslen<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>covcut<span class="pl-pds">&#39;</span></span>]],</td>
      </tr>
      <tr>
        <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
        <td id="LC241" class="blob-code blob-code-inner js-file-line">                       args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>]])</td>
      </tr>
      <tr>
        <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
        <td id="LC242" class="blob-code blob-code-inner js-file-line">    blastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
        <td id="LC243" class="blob-code blob-code-inner js-file-line">    orthPresence_df <span class="pl-k">=</span> getCogsPresent(blastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
        <td id="LC244" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
        <td id="LC245" class="blob-code blob-code-inner js-file-line">    binBlastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
        <td id="LC246" class="blob-code blob-code-inner js-file-line">    binPresence_df <span class="pl-k">=</span> getCogsPresent(binBlastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
        <td id="LC247" class="blob-code blob-code-inner js-file-line">    cogPresence_df <span class="pl-k">=</span> orthPresence_df.append(binPresence_df, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
      </tr>
      <tr>
        <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
        <td id="LC248" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
        <td id="LC249" class="blob-code blob-code-inner js-file-line">    fname <span class="pl-k">=</span> args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]] <span class="pl-k">+</span>args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_cogspresent.csv<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
        <td id="LC250" class="blob-code blob-code-inner js-file-line">    cogPresence_df.to_csv(fname)</td>
      </tr>
      <tr>
        <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
        <td id="LC251" class="blob-code blob-code-inner js-file-line">    current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]])  <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td>
      </tr>
      <tr>
        <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
        <td id="LC252" class="blob-code blob-code-inner js-file-line">    createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]])</td>
      </tr>
      <tr>
        <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
        <td id="LC253" class="blob-code blob-code-inner js-file-line">    createHTML(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
      </tr>
      <tr>
        <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
        <td id="LC254" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
        <td id="LC255" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">test_cluster</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
      </tr>
      <tr>
        <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
        <td id="LC256" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span> (<span class="pl-s"><span class="pl-pds">&quot;</span>name: <span class="pl-c1">%s</span><span class="pl-pds">&quot;</span></span>,args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]])</td>
      </tr>
      <tr>
        <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
        <td id="LC257" class="blob-code blob-code-inner js-file-line">    cogPresence_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">&quot;</span>test_cogspresent.csv<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
        <td id="LC258" class="blob-code blob-code-inner js-file-line">    <span class="pl-c1">print</span>(cogPresence_df)</td>
      </tr>
      <tr>
        <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
        <td id="LC259" class="blob-code blob-code-inner js-file-line">    current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]])  <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td>
      </tr>
      <tr>
        <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
        <td id="LC260" class="blob-code blob-code-inner js-file-line">    createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]])</td>
      </tr>
      <tr>
        <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
        <td id="LC261" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
        <td id="LC262" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">vivax_contigs</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
      </tr>
      <tr>
        <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
        <td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {&#39;name&#39;: 2, &#39;pdfexport&#39;: 3, &#39;contigs&#39;: 4, &#39;html_file&#39;: 5, &#39;html_resource&#39;: 6}</span></td>
      </tr>
      <tr>
        <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
        <td id="LC264" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
        <td id="LC265" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>test_cluster(args,dict)</span></td>
      </tr>
      <tr>
        <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
        <td id="LC266" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>return;</span></td>
      </tr>
      <tr>
        <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
        <td id="LC267" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
        <td id="LC268" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>subprocess.call(&#39;echo $PATH&#39;,shell = True)</span></td>
      </tr>
      <tr>
        <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
        <td id="LC269" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>sys.exit(1)</span></td>
      </tr>
      <tr>
        <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
        <td id="LC270" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
        <td id="LC271" class="blob-code blob-code-inner js-file-line">    vivaxPath <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/data/vivax<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
        <td id="LC272" class="blob-code blob-code-inner js-file-line">    shutil.copyfile(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>contigs<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.fa<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
        <td id="LC273" class="blob-code blob-code-inner js-file-line">    blastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
        <td id="LC274" class="blob-code blob-code-inner js-file-line">    orthPresence_df <span class="pl-k">=</span> getCogsPresent(blastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
        <td id="LC275" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
        <td id="LC276" class="blob-code blob-code-inner js-file-line">    binBlastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
        <td id="LC277" class="blob-code blob-code-inner js-file-line">    binPresence_df <span class="pl-k">=</span> getCogsPresent(binBlastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">&quot;</span></span>)</td>
      </tr>
      <tr>
        <td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
        <td id="LC278" class="blob-code blob-code-inner js-file-line">    cogPresence_df <span class="pl-k">=</span> orthPresence_df.append(binPresence_df, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
      </tr>
      <tr>
        <td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
        <td id="LC279" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
        <td id="LC280" class="blob-code blob-code-inner js-file-line">    fname <span class="pl-k">=</span> args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_cogspresent.csv<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
        <td id="LC281" class="blob-code blob-code-inner js-file-line">    cogPresence_df.to_csv(fname)</td>
      </tr>
      <tr>
        <td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
        <td id="LC282" class="blob-code blob-code-inner js-file-line">    current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]])  <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td>
      </tr>
      <tr>
        <td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
        <td id="LC283" class="blob-code blob-code-inner js-file-line">    createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>]])</td>
      </tr>
      <tr>
        <td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
        <td id="LC284" class="blob-code blob-code-inner js-file-line">    createHTML(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
      </tr>
      <tr>
        <td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
        <td id="LC285" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
        <td id="LC286" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
        <td id="LC287" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>__main__<span class="pl-pds">&quot;</span></span>:</td>
      </tr>
      <tr>
        <td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
        <td id="LC288" class="blob-code blob-code-inner js-file-line">    sys.exit()</td>
      </tr>
      <tr>
        <td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
        <td id="LC289" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
        <td id="LC290" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
        <td id="LC291" class="blob-code blob-code-inner js-file-line">
</td>
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      <tr>
        <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
        <td id="LC292" class="blob-code blob-code-inner js-file-line">
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