comparison Tryp_T.py @ 7:25226d33642e draft

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6:e91e41380946

"""
 * 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 subprocess
import pandas as pd
import re
import os
import sys
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt

pList = ['P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'P9', 'P10', 'P11', 'P12', 'P13', 'P14', 'P15']
quietString = "" #"">> Vap_log.txt 2>&1"
def transcriptMapping(inputname, strain, forwardFN,reverseFN):
    #where is our Reference data -
    dir_path = os.path.dirname(os.path.realpath(__file__))
    refName = dir_path+"/data/Reference/Tc148" #default
    if strain == "Tc148":
        refName = dir_path+"/data/Reference/Tc148"
    if strain == "IL3000":
        refName = dir_path+"/data/Reference/IL3000"
    #argString = "bowtie2 -x Refe4rence/IL3000 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam"    #>log.txt
    #argString = "bowtie2 -x Reference/Tc148 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam"    #>log.txt
    argString = "bowtie2 -x "+refName+" -1 "+forwardFN+" -2 "+reverseFN+" -S "+inputname+".sam"+quietString    #>log.txt
    #print(argString)
    returncode = subprocess.call(argString, shell=True)

def processSamFiles(inputname):
    #debug use a mapping sam file we have already found
    #dir_path = os.path.dirname(os.path.realpath(__file__))
    #bugName = dir_path+"/data/T_Test" #defasult

    cur_path = os.getcwd()
    samName = cur_path+"/"+inputname

    #argString = "samtools view -bS "+bugName+" > "+inputname+".bam"
    argString = "samtools view -bS "+inputname+".sam > "+samName+".bam"+quietString
    #print(argString)
    returncode = subprocess.call(argString, shell=True)


    #argString = "samtools sort "+bugName+" -o "+inputname+".sorted"
    argString = "samtools sort "+samName+".bam -o "+samName+".sorted"+quietString
    #print("argstring = "+argString)
    returncode = subprocess.call(argString, shell=True)

    #argString = "samtools index "+bugName+".sorted "+inputname+".sorted.bai"
    argString = "samtools index "+samName+".sorted "+samName+".sorted.bai"+quietString
    #print("argstring = " + argString)
    returncode = subprocess.call(argString, shell=True)




def transcriptAbundance(inputname, strain):
    dir_path = os.path.dirname(os.path.realpath(__file__))
    refName = dir_path + "/data/Reference/ORFAnnotation.gtf"  # defasult
    if strain == "Tc148":
        refName = dir_path + "/data/Reference/ORFAnnotation.gtf"
    if strain == "IL3000":
        refName = dir_path + "/data/Reference/IL3000.gtf"
    #argString = "cufflinks -G Reference/IL3000.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"
    #argString = "cufflinks -G Reference/ORFAnnotation.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"
    argString = "cufflinks -q -G "+refName+" -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"+quietString
    returncode = subprocess.call(argString, shell = True)


def convertToFasta(inputName, strain):  #equivalent to Sara's awk scripte
    dir_path = os.path.dirname(os.path.realpath(__file__))
    refName = dir_path + "/data/Reference/ORFAnnotation.gtf"  # default
    if strain == "Tc148":
        refName = dir_path + "/data/Reference/148_prot.fasta"
    if strain == "IL3000":
        refName = dir_path + "/data/Reference/IL3000_prot.fasta"

    cuff_df = pd.read_csv(inputName+".cuff/genes.fpkm_tracking", sep='\t')
    cuff_df = cuff_df[(cuff_df['FPKM'] > 0)]
    cuff_df.to_csv("cuffTest.csv")
    gene_id_List = cuff_df['gene_id'].tolist()

    #print(gene_id_List)
    #print ("Found from 8880="+str(found))

    # need to load in IL3000_prot.fasta
    # for each line with >TcIL3000_1_1940
    # search within cuff_df[gene_id] for match
    # add it to the outfile. (need to save it as used by hmmer later
    number = 0
    all = 0
    with open(inputName+"_6frame.fas", 'w') as outfile:
        ref = open(refName,'r')
        #ref = open(r"Reference/IL3000_prot.fasta",'r')
        n = 0
        line = ref.readline()
        while line:
            if line[0] == '>':
                all = all+1
                ln = line[1:]   #remove >
                ln = ln.rstrip()     #remove /n /r etc
                #print (ln)
                if ln in gene_id_List:
                    number = number+1
                    outfile.write(line)
                    line = ref.readline()
                    if line:
                        while line[0] != '>':
                            outfile.write(line)
                            line=ref.readline()
                            if not line:
                                break;
                else:
                    line = ref.readline()
            else:
                line =ref.readline()
    ref.close()
    print(str(len(gene_id_List))+":"+str(number)+" from "+str(all))
    return cuff_df

def HMMerMotifSearch(name, strain, cuff_df):
    motifs = ['1', '2a', '2b', '3', '4a', '4b', '4c', '5', '6', '7', '8a', '8b', '9a', '9b',
              '9c', '10a', '10b', '11a', '11b', '12', '13a', '13b', '13c', '13d', '14', '15a', '15b', '15c']
    dir_path = os.path.dirname(os.path.realpath(__file__))
    phylopath = dir_path + "/data/Motifs/Phylotype"
    lineCounts = []
    compoundList = []
    for m in motifs:
        argString = "hmmsearch "+phylopath + m + ".hmm " + name + "_6frame.fas > Phy" + m + ".out"
        print(argString)
        subprocess.call(argString, shell=True)
        hmmResult = open("Phy" + m + ".out", 'r')
        regex = r"Tc148[0-9]{1,8}"
        if strain == "Tc148":
            regex = r"Tc148[0-9]{1,8}"
        if strain == "IL3000":
            regex = r"TcIL3000_[0-9]{1,4}_[0-9]{1,5}"
        n = 0
        outList = []
        for line in hmmResult:
            m = re.search(regex, line)
            if m:
                outList.append(""+m.group())
                n += 1
            if re.search(r"inclusion", line):
                print("inclusion threshold reached")
                break
        compoundList.append(outList)
        lineCounts.append(n)
        hmmResult.close()
    #print(lineCounts)

    #print(cuff_df)
    concatGroups = [1, 2, 1, 3, 1, 1, 1, 2, 3, 2, 2, 1, 4, 1, 3]
    countList = []
    weightList = []
    countIndex = 0
    totalCount = 0
    totalWeigth = 0
    for c in concatGroups:
        a = []
        weight = []
        for n in range(0, c):
            a = a + compoundList.pop(0)
        t = set(a)
        countList.append(len(t))
        wa = 0
        for w in t:
            wt = cuff_df.loc[cuff_df['gene_id'] == w, 'FPKM'].iloc[0]
            #print(w)
            #print(wt)
            wa = wa+wt
        weightList.append(wa)
        totalWeigth+=wa
        totalCount += len(t)
    countList.append(totalCount)
    weightList.append(totalWeigth)
    #print(countList)
    #print("--------")
    #print(weightList)
    #print("--------")
    return countList,weightList

def relativeFrequencyTable(countList, name, htmlresource):
    relFreqList = []
    c = float(countList[15])
    for i in range(0, 15):
        relFreqList.append(countList[i] / c)

    data = {'Phylotype': pList, 'Relative Frequency': relFreqList}
    relFreq_df = pd.DataFrame(data)
    j_fname = htmlresource+ "/" + name + "_t_relative_frequency.csv"
    relFreq_df.to_csv(j_fname)
    return relFreqList  # 0-14 = p1-p15 counts [15] = total counts


def weightedFrequencyTable(countList, name, htmlresource):
    relFreqList = []
    c = float(countList[15])
    for i in range(0, 15):
        relFreqList.append(countList[i] / c)

    data = {'Phylotype': pList, 'Weighted Frequency': relFreqList}
    relFreq_df = pd.DataFrame(data)
    j_fname = htmlresource+ "/" + name + "_t_weighted_frequency.csv"
    relFreq_df.to_csv(j_fname)
    return relFreqList  # 0-14 = p1-p15 counts [15] = total counts



def createStackedBar(name,freqList,strain,pdf,html_resource):
    palette = ["#0000ff", "#6495ed", "#00ffff", "#caff70",
               "#228b22", "#528b8b", "#00ff00", "#a52a2a",
               "#ff0000", "#ffff00", "#ffa500", "#ff1493",
               "#9400d3", "#bebebe", "#000000", "#ff00ff"]

    VAP_148 = [0.072, 0.032, 0.032, 0.004, 0.007,
               0.005, 0.202, 0.004, 0.006, 0.014,
               0.130, 0.133, 0.054, 0.039, 0.265]

    VAP_IL3000 = [0.073, 0.040, 0.049, 0.018, 0.060,
                  0.055, 0.054, 0.025, 0.012, 0.060,
                  0.142, 0.100, 0.061, 0.078, 0.172]
    cmap = plt.cm.get_cmap('tab20')
    palette = [cmap(i) for i in range(cmap.N)]

    if strain == "Tc148":
        VAPtable = VAP_148
        VAPname='Tc148\nGenome VAP'
    if strain == "IL3000":
        VAPtable = VAP_IL3000
        VAPname= 'IL3000\nGenome VAP'
    width = 0.35  # the width of the bars: can also be len(x) sequence
    plots = []
    fpos = 0
    vpos = 0
    for p in range(0, 15):
        tp = plt.bar(0, freqList[p], width, color= palette[p], bottom = fpos)
        fpos +=freqList[p]

        tp = plt.bar(1, VAPtable[p], width, color= palette[p], bottom = vpos)
        vpos +=VAPtable[p]

        plots.append(tp)
    plt.xticks([0,1],[name,VAPname])
    plt.legend(plots[::-1],['p15','p14','p13','p12','p11','p10','p9','p8','p7','p6','p5','p4','p3','p2','p1'])
    title = "Figure Legend: The transcriptomic Variant Antigen Profile of $\itTrypanosoma$ $\itcongolense$ estimated as phylotype " \
            "proportion adjusted for transcript abundance and the reference genomic Variant Antigen Profile. " \
            "\nData was produced with the 'Variant Antigen Profiler' (Silva Pereira and Jackson, 2018)."
    #plt.title(title, wrap="True")
    #plt.text(-0.2, -0.05, title, va="top", transform=ax.transAxes, wrap="True")
    plt.text(-0.3, -0.15, title, va="top", wrap="True")
    plt.tight_layout(pad=1.5)
    plt.subplots_adjust(bottom = 0.3,top=0.99,left=0.125,right=0.9,hspace=0.2,wspace=0.2)

    plt.savefig(html_resource + "/stackedbar.png")
    if pdf == 'PDF_Yes':
        plt.savefig(html_resource + "/stackedbar.pdf")
    #plt.show()


def createHTML(name,htmlfn,htmlresource,freqList,weightList):
    #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource
    htmlString = r"<html><title>T.congolense VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma congolense</i> Variant Antigen Profile</h2><h3>"
    htmlString += name
    htmlString += r"<br>Transcriptomic Analysis</h3></p>"
    htmlString += "<p style = 'margin-left:20%; margin-right:20%'>Table Legend: Variant Antigen Profiles of a transcriptome of <i>Trypanosoma congolense</i> estimated as phylotype proportion. " \
                  "Weighted frequency refers to the phylotype proportion based transcript abundance. " \
                  "Data was produced with the 'Variant Antigen Profiler' (Silva Pereira and Jackson, 2018).</p> "
    htmlString += r"<style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style>"

    htmlString += r"<table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><th>Relative Frequency</th><th>Weighted Frequency</th></tr>"
    tabString = ""
    # flush out table with correct values
    for i in range(0, 15):
        f = format(freqList[i], '.4f')
        w = format(weightList[i], '.4f')
        tabString += "<tr><td>phy" + str(i + 1) + "</td><td>"  + f + "</td><td>" + w + "</td></tr>"
    htmlString += tabString + "</table><br><br><br><br><br>"
    htmlString += r"<p> <h3>Stacked Bar chart of Phylotype Frequency</h3> The 'weighted' relative frequency of each phylotype alongside the VAP of selected strain.</p>"
    imgString = r"<img src = 'stackedbar.png' alt='Stacked bar chart of phylotype variation' style='max-width:100%'><br><br>"
    htmlString += imgString

#    htmlString += r"<p><h3>The Deviation Heat Map and Dendogram</h3>The phylotype variation expressed as the deviation from your sample mean compared to the model dataset</p>"
#    imgString = r"<img src = 'dheatmap.png' alt='Deviation Heatmap' style='max-width:100%'><br><br>"
#    htmlString += imgString

#    htmlString += r"<p><h3>The Variation PCA plot</h3>PCA analysis corresponding to absolute variation. Colour coded according to location</p>"
#    imgString = r"<img src = 'vapPCA.png' alt='PCA Analysis' style='max-width:100%'><br><br>"
#    htmlString += imgString + r"</div></body></html>"

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

#argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}
def transcriptomicProcess(args,dict):
    transcriptMapping(args[dict['name']], args[dict['strain']], args[dict['forward']], args[dict['reverse']])        #uses bowtie
    processSamFiles(args[dict['name']])                              #uses samtools
    transcriptAbundance(args[dict['name']],args[dict['strain']])                          #uses cufflinks -> ?.cuff/*.*
    cuff_df = convertToFasta(args[dict['name']],args[dict['strain']])
    countList, weightList = HMMerMotifSearch(args[dict['name']],args[dict['strain']], cuff_df)
    relFreqList = relativeFrequencyTable(countList,args[dict['name']],args[dict['html_resource']])
    relWeightList = weightedFrequencyTable(weightList,args[dict['name']],args[dict['html_resource']])
    createStackedBar(args[dict['name']],relWeightList, args[dict['strain']],args[dict['pdfexport']],args[dict['html_resource']])
    createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']], relFreqList, relWeightList)

if __name__ == "__main__":
    #print("Commencing Transcript Mapping")
    #transcriptMapping("T_Test", "Transcripts.1","Transcripts.2")
    #print("Processimg Sam Files")
    #processSamFiles("T_Test")
    #print("Assessing Transcript Abundance")
    #transcriptAbundance("T_Test")
    #print ("Converting to Fasta Subset")
    #cuff_df = convertToFasta("T_Test")
    #print("Commencing HMMer search")
    #countList, weightList = HMMerMotifSearch("T_Test",cuff_df)
    #relativeFrequencyTable(countList,'T_Test')
    #weightedFrequencyTable(weightList,'T_Test')
    relFreqList = [0.111842105,0.059210526,0.026315789,0.013157895,
                   0.006578947,0.013157895,0.032894737,0.019736842,
                   0.039473684,0.046052632,0.217105263,0.065789474,
                   0.151315789,0.059210526,0.138157895]

    relWeightList = [0.07532571,0.05900545,0.009601452,0.042357532,0.01236219,0.001675663,0.04109726,
                     0.097464248,0.057491666,0.05826875,0.279457473,0.070004772,0.065329007,0.085361298,0.045197529]

    createStackedBar('T_Test',relWeightList, 'Tc148','PDF_Yes','results')
    createHTML("t_test","results/t_test.html","results",relFreqList,relWeightList)

7:25226d33642e

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        <td id="LC26" 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="L27" class="blob-num js-line-number" data-line-number="27"></td>
        <td id="LC27" 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 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"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td>
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      <tr>
        <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
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</td>
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        <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">pList <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>P1<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P2<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P3<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P4<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P5<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P6<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P7<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P8<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P9<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P10<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P11<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P12<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P13<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P14<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P15<span class="pl-pds">&#39;</span></span>]</td>
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        <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">quietString <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-c"><span class="pl-c">#</span>&quot;&quot;&gt;&gt; Vap_log.txt 2&gt;&amp;1&quot;</span></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">def</span> <span class="pl-en">transcriptMapping</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">strain</span>, <span class="pl-smi">forwardFN</span>,<span class="pl-smi">reverseFN</span>):</td>
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      <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-c"><span class="pl-c">#</span>where is our Reference data -</span></td>
      </tr>
      <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">    dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</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">    refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/Tc148<span class="pl-pds">&quot;</span></span> <span class="pl-c"><span class="pl-c">#</span>default</span></td>
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      <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-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></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">        refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/Tc148<span class="pl-pds">&quot;</span></span></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-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</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">        refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/IL3000<span class="pl-pds">&quot;</span></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-c"><span class="pl-c">#</span>argString = &quot;bowtie2 -x Refe4rence/IL3000 -1 data/&quot;+forwardFN+&quot; -2 data/&quot;+reverseFN+&quot; -S &quot;+inputname+&quot;.sam&quot;    #&gt;log.txt</span></td>
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      <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-c"><span class="pl-c">#</span>argString = &quot;bowtie2 -x Reference/Tc148 -1 data/&quot;+forwardFN+&quot; -2 data/&quot;+reverseFN+&quot; -S &quot;+inputname+&quot;.sam&quot;    #&gt;log.txt</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>bowtie2 -x <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -1 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>forwardFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -2 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>reverseFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -S <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sam<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString    <span class="pl-c"><span class="pl-c">#</span>&gt;log.txt</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>print(argString)</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">    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="L45" class="blob-num js-line-number" data-line-number="45"></td>
        <td id="LC45" class="blob-code blob-code-inner js-file-line">
</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"><span class="pl-k">def</span> <span class="pl-en">processSamFiles</span>(<span class="pl-smi">inputname</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-c"><span class="pl-c">#</span>debug use a mapping sam file we have already found</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-c"><span class="pl-c">#</span>dir_path = os.path.dirname(os.path.realpath(__file__))</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">    <span class="pl-c"><span class="pl-c">#</span>bugName = dir_path+&quot;/data/T_Test&quot; #defasult</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">
</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">    cur_path <span class="pl-k">=</span> os.getcwd()</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">    samName <span class="pl-k">=</span> cur_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>inputname</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">
</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-c"><span class="pl-c">#</span>argString = &quot;samtools view -bS &quot;+bugName+&quot; &gt; &quot;+inputname+&quot;.bam&quot;</span></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">    argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools view -bS <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sam &gt; <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.bam<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</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>print(argString)</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">    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="L58" class="blob-num js-line-number" data-line-number="58"></td>
        <td id="LC58" class="blob-code blob-code-inner js-file-line">
</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">
</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">    <span class="pl-c"><span class="pl-c">#</span>argString = &quot;samtools sort &quot;+bugName+&quot; -o &quot;+inputname+&quot;.sorted&quot;</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">    argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools sort <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.bam -o <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</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-c"><span class="pl-c">#</span>print(&quot;argstring = &quot;+argString)</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">    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="L64" class="blob-num js-line-number" data-line-number="64"></td>
        <td id="LC64" class="blob-code blob-code-inner js-file-line">
</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>argString = &quot;samtools index &quot;+bugName+&quot;.sorted &quot;+inputname+&quot;.sorted.bai&quot;</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">    argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools index <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted.bai<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</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">    <span class="pl-c"><span class="pl-c">#</span>print(&quot;argstring = &quot; + argString)</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">    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="L69" class="blob-num js-line-number" data-line-number="69"></td>
        <td id="LC69" class="blob-code blob-code-inner js-file-line">
</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">
</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"><span class="pl-k">def</span> <span class="pl-en">transcriptAbundance</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">strain</span>):</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">    dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</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">    refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">&quot;</span></span>  <span class="pl-c"><span class="pl-c">#</span> defasult</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">    <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></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">        refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">&quot;</span></span></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">    <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</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">        refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/IL3000.gtf<span class="pl-pds">&quot;</span></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">    <span class="pl-c"><span class="pl-c">#</span>argString = &quot;cufflinks -G Reference/IL3000.gtf -o &quot;+inputname+&quot;.cuff -u -p 8 &quot;+inputname+&quot;.sorted&quot;</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">    <span class="pl-c"><span class="pl-c">#</span>argString = &quot;cufflinks -G Reference/ORFAnnotation.gtf -o &quot;+inputname+&quot;.cuff -u -p 8 &quot;+inputname+&quot;.sorted&quot;</span></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">    argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>cufflinks -q -G <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -o <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.cuff -u -p 8 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</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">    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="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">
</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"><span class="pl-k">def</span> <span class="pl-en">convertToFasta</span>(<span class="pl-smi">inputName</span>, <span class="pl-smi">strain</span>):  <span class="pl-c"><span class="pl-c">#</span>equivalent to Sara&#39;s awk scripte</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">    dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__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">    refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">&quot;</span></span>  <span class="pl-c"><span class="pl-c">#</span> default</span></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">    <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></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">        refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/148_prot.fasta<span class="pl-pds">&quot;</span></span></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">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</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">        refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/IL3000_prot.fasta<span class="pl-pds">&quot;</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">
</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">    cuff_df <span class="pl-k">=</span> pd.read_csv(inputName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.cuff/genes.fpkm_tracking<span class="pl-pds">&quot;</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span><span class="pl-cce">\t</span><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">    cuff_df <span class="pl-k">=</span> cuff_df[(cuff_df[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>] <span class="pl-k">&gt;</span> <span class="pl-c1">0</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">    cuff_df.to_csv(<span class="pl-s"><span class="pl-pds">&quot;</span>cuffTest.csv<span class="pl-pds">&quot;</span></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">    gene_id_List <span class="pl-k">=</span> cuff_df[<span class="pl-s"><span class="pl-pds">&#39;</span>gene_id<span class="pl-pds">&#39;</span></span>].tolist()</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(gene_id_List)</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 (&quot;Found from 8880=&quot;+str(found))</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">
</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">    <span class="pl-c"><span class="pl-c">#</span> need to load in IL3000_prot.fasta</span></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> for each line with &gt;TcIL3000_1_1940</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-c"><span class="pl-c">#</span> search within cuff_df[gene_id] for match</span></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">    <span class="pl-c"><span class="pl-c">#</span> add it to the outfile. (need to save it as used by hmmer later</span></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">    number <span class="pl-k">=</span> <span class="pl-c1">0</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">    <span class="pl-c1">all</span> <span class="pl-k">=</span> <span class="pl-c1">0</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">    <span class="pl-k">with</span> <span class="pl-c1">open</span>(inputName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_6frame.fas<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>w<span class="pl-pds">&#39;</span></span>) <span class="pl-k">as</span> outfile:</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">        ref <span class="pl-k">=</span> <span class="pl-c1">open</span>(refName,<span class="pl-s"><span class="pl-pds">&#39;</span>r<span class="pl-pds">&#39;</span></span>)</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">        <span class="pl-c"><span class="pl-c">#</span>ref = open(r&quot;Reference/IL3000_prot.fasta&quot;,&#39;r&#39;)</span></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">        n <span class="pl-k">=</span> <span class="pl-c1">0</span></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">        line <span class="pl-k">=</span> ref.readline()</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-k">while</span> line:</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-k">if</span> line[<span class="pl-c1">0</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>&gt;<span class="pl-pds">&#39;</span></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">                <span class="pl-c1">all</span> <span class="pl-k">=</span> <span class="pl-c1">all</span><span class="pl-k">+</span><span class="pl-c1">1</span></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">                ln <span class="pl-k">=</span> line[<span class="pl-c1">1</span>:]   <span class="pl-c"><span class="pl-c">#</span>remove &gt;</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">                ln <span class="pl-k">=</span> ln.rstrip()     <span class="pl-c"><span class="pl-c">#</span>remove /n /r etc</span></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-c"><span class="pl-c">#</span>print (ln)</span></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">                <span class="pl-k">if</span> ln <span class="pl-k">in</span> gene_id_List:</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">                    number <span class="pl-k">=</span> number<span class="pl-k">+</span><span class="pl-c1">1</span></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">                    outfile.write(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">                    line <span class="pl-k">=</span> ref.readline()</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">if</span> line:</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-k">while</span> line[<span class="pl-c1">0</span>] <span class="pl-k">!=</span> <span class="pl-s"><span class="pl-pds">&#39;</span>&gt;<span class="pl-pds">&#39;</span></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">                            outfile.write(line)</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">                            line<span class="pl-k">=</span>ref.readline()</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">                            <span class="pl-k">if</span> <span class="pl-k">not</span> line:</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">                                <span class="pl-k">break</span><span class="pl-bu">;</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-k">else</span>:</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">                    line <span class="pl-k">=</span> ref.readline()</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">            <span class="pl-k">else</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">                line <span class="pl-k">=</span>ref.readline()</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">    ref.close()</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">    <span class="pl-c1">print</span>(<span class="pl-c1">str</span>(<span class="pl-c1">len</span>(gene_id_List))<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><span class="pl-c1">str</span>(number)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> from <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(<span class="pl-c1">all</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">return</span> cuff_df</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">
</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"><span class="pl-k">def</span> <span class="pl-en">HMMerMotifSearch</span>(<span class="pl-smi">name</span>, <span class="pl-smi">strain</span>, <span class="pl-smi">cuff_df</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">    motifs <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>1<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>2a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>2b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>3<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>5<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>6<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>7<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>8a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>8b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>9a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>9b<span class="pl-pds">&#39;</span></span>,</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">              <span class="pl-s"><span class="pl-pds">&#39;</span>9c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>10a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>10b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>11a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>11b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>12<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13d<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>14<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15c<span class="pl-pds">&#39;</span></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">    dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</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">    phylopath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Motifs/Phylotype<span class="pl-pds">&quot;</span></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">    lineCounts <span class="pl-k">=</span> []</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">    compoundList <span class="pl-k">=</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-k">for</span> m <span class="pl-k">in</span> motifs:</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">        argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>hmmsearch <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>phylopath <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.hmm <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>_6frame.fas &gt; Phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.out<span class="pl-pds">&quot;</span></span></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-c1">print</span>(argString)</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">        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="L148" class="blob-num js-line-number" data-line-number="148"></td>
        <td id="LC148" class="blob-code blob-code-inner js-file-line">        hmmResult <span class="pl-k">=</span> <span class="pl-c1">open</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>Phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.out<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>r<span class="pl-pds">&#39;</span></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">        regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>Tc148[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,8}</span><span class="pl-pds">&quot;</span></span></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">        <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></span>:</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">            regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>Tc148[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,8}</span><span class="pl-pds">&quot;</span></span></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-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</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">            regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>TcIL3000_[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,4}</span>_[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,5}</span><span class="pl-pds">&quot;</span></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">        n <span class="pl-k">=</span> <span class="pl-c1">0</span></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">        outList <span class="pl-k">=</span> []</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">        <span class="pl-k">for</span> line <span class="pl-k">in</span> hmmResult:</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">            m <span class="pl-k">=</span> re.search(regex, line)</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-k">if</span> m:</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">                outList.append(<span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>m.group())</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">                n <span class="pl-k">+=</span> <span class="pl-c1">1</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-k">if</span> re.search(<span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>inclusion<span class="pl-pds">&quot;</span></span>, line):</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-c1">print</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>inclusion threshold reached<span class="pl-pds">&quot;</span></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">                <span class="pl-k">break</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">        compoundList.append(outList)</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">        lineCounts.append(n)</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">        hmmResult.close()</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">    <span class="pl-c"><span class="pl-c">#</span>print(lineCounts)</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">
</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">    <span class="pl-c"><span class="pl-c">#</span>print(cuff_df)</span></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">    concatGroups <span class="pl-k">=</span> [<span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">3</span>, <span class="pl-c1">2</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">4</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</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">    countList <span class="pl-k">=</span> []</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">    weightList <span class="pl-k">=</span> []</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">    countIndex <span class="pl-k">=</span> <span class="pl-c1">0</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">    totalCount <span class="pl-k">=</span> <span class="pl-c1">0</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">    totalWeigth <span class="pl-k">=</span> <span class="pl-c1">0</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-k">for</span> c <span class="pl-k">in</span> concatGroups:</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">        a <span class="pl-k">=</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">        weight <span class="pl-k">=</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">        <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, c):</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">            a <span class="pl-k">=</span> a <span class="pl-k">+</span> compoundList.pop(<span class="pl-c1">0</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">        t <span class="pl-k">=</span> <span class="pl-c1">set</span>(a)</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">        countList.append(<span class="pl-c1">len</span>(t))</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">        wa <span class="pl-k">=</span> <span class="pl-c1">0</span></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">        <span class="pl-k">for</span> w <span class="pl-k">in</span> t:</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">            wt <span class="pl-k">=</span> cuff_df.loc[cuff_df[<span class="pl-s"><span class="pl-pds">&#39;</span>gene_id<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> w, <span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>].iloc[<span class="pl-c1">0</span>]</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">            <span class="pl-c"><span class="pl-c">#</span>print(w)</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">            <span class="pl-c"><span class="pl-c">#</span>print(wt)</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">            wa <span class="pl-k">=</span> wa<span class="pl-k">+</span>wt</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">        weightList.append(wa)</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">        totalWeigth<span class="pl-k">+=</span>wa</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">        totalCount <span class="pl-k">+=</span> <span class="pl-c1">len</span>(t)</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">    countList.append(totalCount)</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">    weightList.append(totalWeigth)</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">    <span class="pl-c"><span class="pl-c">#</span>print(countList)</span></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">    <span class="pl-c"><span class="pl-c">#</span>print(&quot;--------&quot;)</span></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">    <span class="pl-c"><span class="pl-c">#</span>print(weightList)</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">    <span class="pl-c"><span class="pl-c">#</span>print(&quot;--------&quot;)</span></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">    <span class="pl-k">return</span> countList,weightList</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"><span class="pl-k">def</span> <span class="pl-en">relativeFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</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">    relFreqList <span class="pl-k">=</span> []</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">    c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</span>])</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">    <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">15</span>):</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">        relFreqList.append(countList[i] <span class="pl-k">/</span> c)</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">
</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">    data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>: pList, <span class="pl-s"><span class="pl-pds">&#39;</span>Relative Frequency<span class="pl-pds">&#39;</span></span>: relFreqList}</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">    relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</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">    j_fname <span class="pl-k">=</span> htmlresource<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>_t_relative_frequency.csv<span class="pl-pds">&quot;</span></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">    relFreq_df.to_csv(j_fname)</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-k">return</span> relFreqList  <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</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">
</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">
</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"><span class="pl-k">def</span> <span class="pl-en">weightedFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</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">    relFreqList <span class="pl-k">=</span> []</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">    c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</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">    <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">15</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">        relFreqList.append(countList[i] <span class="pl-k">/</span> c)</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">
</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">    data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>: pList, <span class="pl-s"><span class="pl-pds">&#39;</span>Weighted Frequency<span class="pl-pds">&#39;</span></span>: relFreqList}</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">    relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</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">    j_fname <span class="pl-k">=</span> htmlresource<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>_t_weighted_frequency.csv<span class="pl-pds">&quot;</span></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">    relFreq_df.to_csv(j_fname)</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">    <span class="pl-k">return</span> relFreqList  <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></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">
</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"><span class="pl-k">def</span> <span class="pl-en">createStackedBar</span>(<span class="pl-smi">name</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">strain</span>,<span class="pl-smi">pdf</span>,<span class="pl-smi">html_resource</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">    palette <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&quot;</span>#0000ff<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#6495ed<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#00ffff<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#caff70<span class="pl-pds">&quot;</span></span>,</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-s"><span class="pl-pds">&quot;</span>#228b22<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#528b8b<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#00ff00<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#a52a2a<span class="pl-pds">&quot;</span></span>,</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">               <span class="pl-s"><span class="pl-pds">&quot;</span>#ff0000<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#ffff00<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#ffa500<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#ff1493<span class="pl-pds">&quot;</span></span>,</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-s"><span class="pl-pds">&quot;</span>#9400d3<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#bebebe<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#000000<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#ff00ff<span class="pl-pds">&quot;</span></span>]</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">
</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">    <span class="pl-c1">VAP_148</span> <span class="pl-k">=</span> [<span class="pl-c1">0.072</span>, <span class="pl-c1">0.032</span>, <span class="pl-c1">0.032</span>, <span class="pl-c1">0.004</span>, <span class="pl-c1">0.007</span>,</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">               <span class="pl-c1">0.005</span>, <span class="pl-c1">0.202</span>, <span class="pl-c1">0.004</span>, <span class="pl-c1">0.006</span>, <span class="pl-c1">0.014</span>,</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-c1">0.130</span>, <span class="pl-c1">0.133</span>, <span class="pl-c1">0.054</span>, <span class="pl-c1">0.039</span>, <span class="pl-c1">0.265</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">
</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-c1">VAP_IL3000</span> <span class="pl-k">=</span> [<span class="pl-c1">0.073</span>, <span class="pl-c1">0.040</span>, <span class="pl-c1">0.049</span>, <span class="pl-c1">0.018</span>, <span class="pl-c1">0.060</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">                  <span class="pl-c1">0.055</span>, <span class="pl-c1">0.054</span>, <span class="pl-c1">0.025</span>, <span class="pl-c1">0.012</span>, <span class="pl-c1">0.060</span>,</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">                  <span class="pl-c1">0.142</span>, <span class="pl-c1">0.100</span>, <span class="pl-c1">0.061</span>, <span class="pl-c1">0.078</span>, <span class="pl-c1">0.172</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">    cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">&#39;</span>tab20<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">    palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</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">
</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">    <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<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">        VAPtable <span class="pl-k">=</span> <span class="pl-c1">VAP_148</span></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">        VAPname<span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>Tc148<span class="pl-cce">\n</span>Genome VAP<span class="pl-pds">&#39;</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">    <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<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">        VAPtable <span class="pl-k">=</span> <span class="pl-c1">VAP_IL3000</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">        VAPname<span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&#39;</span>IL3000<span class="pl-cce">\n</span>Genome VAP<span class="pl-pds">&#39;</span></span></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">    width <span class="pl-k">=</span> <span class="pl-c1">0.35</span>  <span class="pl-c"><span class="pl-c">#</span> the width of the bars: can also be len(x) sequence</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">    plots <span class="pl-k">=</span> []</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">    fpos <span class="pl-k">=</span> <span class="pl-c1">0</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">    vpos <span class="pl-k">=</span> <span class="pl-c1">0</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">    <span class="pl-k">for</span> p <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</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">        tp <span class="pl-k">=</span> plt.bar(<span class="pl-c1">0</span>, freqList[p], width, <span class="pl-v">color</span><span class="pl-k">=</span> palette[p], <span class="pl-v">bottom</span> <span class="pl-k">=</span> fpos)</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">        fpos <span class="pl-k">+=</span>freqList[p]</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">
</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">        tp <span class="pl-k">=</span> plt.bar(<span class="pl-c1">1</span>, VAPtable[p], width, <span class="pl-v">color</span><span class="pl-k">=</span> palette[p], <span class="pl-v">bottom</span> <span class="pl-k">=</span> vpos)</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">        vpos <span class="pl-k">+=</span>VAPtable[p]</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">
</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">        plots.append(tp)</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">    plt.xticks([<span class="pl-c1">0</span>,<span class="pl-c1">1</span>],[name,VAPname])</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">    plt.legend(plots[::<span class="pl-k">-</span><span class="pl-c1">1</span>],[<span class="pl-s"><span class="pl-pds">&#39;</span>p15<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p14<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p13<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p12<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p11<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p10<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p9<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p8<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p7<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p6<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p5<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p4<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p3<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p2<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p1<span class="pl-pds">&#39;</span></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">    title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Figure Legend: The transcriptomic Variant Antigen Profile of $\itTrypanosoma$ $\itcongolense$ estimated as phylotype <span class="pl-pds">&quot;</span></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">            <span class="pl-s"><span class="pl-pds">&quot;</span>proportion adjusted for transcript abundance and the reference genomic Variant Antigen Profile. <span class="pl-pds">&quot;</span></span> \</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-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span>Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</span></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>plt.title(title, wrap=&quot;True&quot;)</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">    <span class="pl-c"><span class="pl-c">#</span>plt.text(-0.2, -0.05, title, va=&quot;top&quot;, transform=ax.transAxes, wrap=&quot;True&quot;)</span></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">    plt.text(<span class="pl-k">-</span><span class="pl-c1">0.3</span>, <span class="pl-k">-</span><span class="pl-c1">0.15</span>, title, <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="L269" class="blob-num js-line-number" data-line-number="269"></td>
        <td id="LC269" class="blob-code blob-code-inner js-file-line">    plt.tight_layout(<span class="pl-v">pad</span><span class="pl-k">=</span><span class="pl-c1">1.5</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">    plt.subplots_adjust(<span class="pl-v">bottom</span> <span class="pl-k">=</span> <span class="pl-c1">0.3</span>,<span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.99</span>,<span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.125</span>,<span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>,<span class="pl-v">hspace</span><span class="pl-k">=</span><span class="pl-c1">0.2</span>,<span class="pl-v">wspace</span><span class="pl-k">=</span><span class="pl-c1">0.2</span>)</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">
</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">    plt.savefig(html_resource <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/stackedbar.png<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">    <span class="pl-k">if</span> pdf <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="L274" class="blob-num js-line-number" data-line-number="274"></td>
        <td id="LC274" class="blob-code blob-code-inner js-file-line">        plt.savefig(html_resource <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/stackedbar.pdf<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">    <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></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">
</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">
</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"><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">htmlresource</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">weightList</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">    <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="L280" class="blob-num js-line-number" data-line-number="280"></td>
        <td id="LC280" 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>congolense VAP&lt;/title&gt;&lt;body&gt;&lt;div style=&#39;text-align:center&#39;&gt;&lt;h2&gt;&lt;i&gt;Trypanosoma congolense&lt;/i&gt; Variant Antigen Profile&lt;/h2&gt;&lt;h3&gt;<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">    htmlString <span class="pl-k">+=</span> name</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">    htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;br&gt;Transcriptomic Analysis&lt;/h3&gt;&lt;/p&gt;<span class="pl-pds">&quot;</span></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">    htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;p style = &#39;margin-left:20%; margin-right:20%&#39;&gt;Table Legend: Variant Antigen Profiles of a transcriptome of &lt;i&gt;Trypanosoma congolense&lt;/i&gt; estimated as phylotype proportion. <span class="pl-pds">&quot;</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">                  <span class="pl-s"><span class="pl-pds">&quot;</span>Weighted frequency refers to the phylotype proportion based transcript abundance. <span class="pl-pds">&quot;</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">                  <span class="pl-s"><span class="pl-pds">&quot;</span>Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).&lt;/p&gt; <span class="pl-pds">&quot;</span></span></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">    htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;style&gt; table, th, tr, td {border: 1px solid black; border-collapse: collapse;}&lt;/style&gt;<span class="pl-pds">&quot;</span></span></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">
</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">    htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;table style=&#39;width:50%;margin-left:25%;text-align:center&#39;&gt;&lt;tr&gt;&lt;th&gt;Phylotype&lt;/th&gt;&lt;th&gt;Relative Frequency&lt;/th&gt;&lt;th&gt;Weighted Frequency&lt;/th&gt;&lt;/tr&gt;<span class="pl-pds">&quot;</span></span></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">    tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span></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">    <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></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">    <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">15</span>):</td>
      </tr>
      <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">        f <span class="pl-k">=</span> <span class="pl-c1">format</span>(freqList[i], <span class="pl-s"><span class="pl-pds">&#39;</span>.4f<span class="pl-pds">&#39;</span></span>)</td>
      </tr>
      <tr>
        <td id="L293" class="blob-num js-line-number" data-line-number="293"></td>
        <td id="LC293" class="blob-code blob-code-inner js-file-line">        w <span class="pl-k">=</span> <span class="pl-c1">format</span>(weightList[i], <span class="pl-s"><span class="pl-pds">&#39;</span>.4f<span class="pl-pds">&#39;</span></span>)</td>
      </tr>
      <tr>
        <td id="L294" class="blob-num js-line-number" data-line-number="294"></td>
        <td id="LC294" class="blob-code blob-code-inner js-file-line">        tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;tr&gt;&lt;td&gt;phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(i <span class="pl-k">+</span> <span class="pl-c1">1</span>) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span>  <span class="pl-k">+</span> f <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> w <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;/tr&gt;<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L295" class="blob-num js-line-number" data-line-number="295"></td>
        <td id="LC295" class="blob-code blob-code-inner js-file-line">    htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/table&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L296" class="blob-num js-line-number" data-line-number="296"></td>
        <td id="LC296" 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;p&gt; &lt;h3&gt;Stacked Bar chart of Phylotype Frequency&lt;/h3&gt; The &#39;weighted&#39; relative frequency of each phylotype alongside the VAP of selected strain<span class="pl-c1">.</span>&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
      </tr>
      <tr>
        <td id="L297" class="blob-num js-line-number" data-line-number="297"></td>
        <td id="LC297" 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;stackedbar<span class="pl-c1">.</span>png&#39; alt=&#39;Stacked bar chart of phylotype variation&#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="L298" class="blob-num js-line-number" data-line-number="298"></td>
        <td id="LC298" class="blob-code blob-code-inner js-file-line">    htmlString <span class="pl-k">+=</span> imgString</td>
      </tr>
      <tr>
        <td id="L299" class="blob-num js-line-number" data-line-number="299"></td>
        <td id="LC299" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L300" class="blob-num js-line-number" data-line-number="300"></td>
        <td id="LC300" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>    htmlString += r&quot;&lt;p&gt;&lt;h3&gt;The Deviation Heat Map and Dendogram&lt;/h3&gt;The phylotype variation expressed as the deviation from your sample mean compared to the model dataset&lt;/p&gt;&quot;</span></td>
      </tr>
      <tr>
        <td id="L301" class="blob-num js-line-number" data-line-number="301"></td>
        <td id="LC301" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>    imgString = r&quot;&lt;img src = &#39;dheatmap.png&#39; alt=&#39;Deviation Heatmap&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;&quot;</span></td>
      </tr>
      <tr>
        <td id="L302" class="blob-num js-line-number" data-line-number="302"></td>
        <td id="LC302" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>    htmlString += imgString</span></td>
      </tr>
      <tr>
        <td id="L303" class="blob-num js-line-number" data-line-number="303"></td>
        <td id="LC303" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L304" class="blob-num js-line-number" data-line-number="304"></td>
        <td id="LC304" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>    htmlString += r&quot;&lt;p&gt;&lt;h3&gt;The Variation PCA plot&lt;/h3&gt;PCA analysis corresponding to absolute variation. Colour coded according to location&lt;/p&gt;&quot;</span></td>
      </tr>
      <tr>
        <td id="L305" class="blob-num js-line-number" data-line-number="305"></td>
        <td id="LC305" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>    imgString = r&quot;&lt;img src = &#39;vapPCA.png&#39; alt=&#39;PCA Analysis&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;&quot;</span></td>
      </tr>
      <tr>
        <td id="L306" class="blob-num js-line-number" data-line-number="306"></td>
        <td id="LC306" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>    htmlString += imgString + r&quot;&lt;/div&gt;&lt;/body&gt;&lt;/html&gt;&quot;</span></td>
      </tr>
      <tr>
        <td id="L307" class="blob-num js-line-number" data-line-number="307"></td>
        <td id="LC307" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L308" class="blob-num js-line-number" data-line-number="308"></td>
        <td id="LC308" 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="L309" class="blob-num js-line-number" data-line-number="309"></td>
        <td id="LC309" class="blob-code blob-code-inner js-file-line">        htmlfile.write(htmlString)</td>
      </tr>
      <tr>
        <td id="L310" class="blob-num js-line-number" data-line-number="310"></td>
        <td id="LC310" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L311" class="blob-num js-line-number" data-line-number="311"></td>
        <td id="LC311" 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;strain&#39;: 4, &#39;forward&#39;: 5, &#39;reverse&#39;: 6, &#39;html_file&#39;: 7, &#39;html_resource&#39;: 8}</span></td>
      </tr>
      <tr>
        <td id="L312" class="blob-num js-line-number" data-line-number="312"></td>
        <td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptomicProcess</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
      </tr>
      <tr>
        <td id="L313" class="blob-num js-line-number" data-line-number="313"></td>
        <td id="LC313" class="blob-code blob-code-inner js-file-line">    transcriptMapping(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>strain<span class="pl-pds">&#39;</span></span>]], 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>]])        <span class="pl-c"><span class="pl-c">#</span>uses bowtie</span></td>
      </tr>
      <tr>
        <td id="L314" class="blob-num js-line-number" data-line-number="314"></td>
        <td id="LC314" class="blob-code blob-code-inner js-file-line">    processSamFiles(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>uses samtools</span></td>
      </tr>
      <tr>
        <td id="L315" class="blob-num js-line-number" data-line-number="315"></td>
        <td id="LC315" class="blob-code blob-code-inner js-file-line">    transcriptAbundance(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>strain<span class="pl-pds">&#39;</span></span>]])                          <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -&gt; ?.cuff/*.*</span></td>
      </tr>
      <tr>
        <td id="L316" class="blob-num js-line-number" data-line-number="316"></td>
        <td id="LC316" class="blob-code blob-code-inner js-file-line">    cuff_df <span class="pl-k">=</span> convertToFasta(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>strain<span class="pl-pds">&#39;</span></span>]])</td>
      </tr>
      <tr>
        <td id="L317" class="blob-num js-line-number" data-line-number="317"></td>
        <td id="LC317" class="blob-code blob-code-inner js-file-line">    countList, weightList <span class="pl-k">=</span> HMMerMotifSearch(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>strain<span class="pl-pds">&#39;</span></span>]], cuff_df)</td>
      </tr>
      <tr>
        <td id="L318" class="blob-num js-line-number" data-line-number="318"></td>
        <td id="LC318" class="blob-code blob-code-inner js-file-line">    relFreqList <span class="pl-k">=</span> relativeFrequencyTable(countList,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>]])</td>
      </tr>
      <tr>
        <td id="L319" class="blob-num js-line-number" data-line-number="319"></td>
        <td id="LC319" class="blob-code blob-code-inner js-file-line">    relWeightList <span class="pl-k">=</span> weightedFrequencyTable(weightList,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>]])</td>
      </tr>
      <tr>
        <td id="L320" class="blob-num js-line-number" data-line-number="320"></td>
        <td id="LC320" class="blob-code blob-code-inner js-file-line">    createStackedBar(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],relWeightList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>strain<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>]],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="L321" class="blob-num js-line-number" data-line-number="321"></td>
        <td id="LC321" 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>]], relFreqList, relWeightList)</td>
      </tr>
      <tr>
        <td id="L322" class="blob-num js-line-number" data-line-number="322"></td>
        <td id="LC322" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L323" class="blob-num js-line-number" data-line-number="323"></td>
        <td id="LC323" 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="L324" class="blob-num js-line-number" data-line-number="324"></td>
        <td id="LC324" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print(&quot;Commencing Transcript Mapping&quot;)</span></td>
      </tr>
      <tr>
        <td id="L325" class="blob-num js-line-number" data-line-number="325"></td>
        <td id="LC325" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>transcriptMapping(&quot;T_Test&quot;, &quot;Transcripts.1&quot;,&quot;Transcripts.2&quot;)</span></td>
      </tr>
      <tr>
        <td id="L326" class="blob-num js-line-number" data-line-number="326"></td>
        <td id="LC326" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print(&quot;Processimg Sam Files&quot;)</span></td>
      </tr>
      <tr>
        <td id="L327" class="blob-num js-line-number" data-line-number="327"></td>
        <td id="LC327" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>processSamFiles(&quot;T_Test&quot;)</span></td>
      </tr>
      <tr>
        <td id="L328" class="blob-num js-line-number" data-line-number="328"></td>
        <td id="LC328" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print(&quot;Assessing Transcript Abundance&quot;)</span></td>
      </tr>
      <tr>
        <td id="L329" class="blob-num js-line-number" data-line-number="329"></td>
        <td id="LC329" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>transcriptAbundance(&quot;T_Test&quot;)</span></td>
      </tr>
      <tr>
        <td id="L330" class="blob-num js-line-number" data-line-number="330"></td>
        <td id="LC330" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print (&quot;Converting to Fasta Subset&quot;)</span></td>
      </tr>
      <tr>
        <td id="L331" class="blob-num js-line-number" data-line-number="331"></td>
        <td id="LC331" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>cuff_df = convertToFasta(&quot;T_Test&quot;)</span></td>
      </tr>
      <tr>
        <td id="L332" class="blob-num js-line-number" data-line-number="332"></td>
        <td id="LC332" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>print(&quot;Commencing HMMer search&quot;)</span></td>
      </tr>
      <tr>
        <td id="L333" class="blob-num js-line-number" data-line-number="333"></td>
        <td id="LC333" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>countList, weightList = HMMerMotifSearch(&quot;T_Test&quot;,cuff_df)</span></td>
      </tr>
      <tr>
        <td id="L334" class="blob-num js-line-number" data-line-number="334"></td>
        <td id="LC334" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>relativeFrequencyTable(countList,&#39;T_Test&#39;)</span></td>
      </tr>
      <tr>
        <td id="L335" class="blob-num js-line-number" data-line-number="335"></td>
        <td id="LC335" class="blob-code blob-code-inner js-file-line">    <span class="pl-c"><span class="pl-c">#</span>weightedFrequencyTable(weightList,&#39;T_Test&#39;)</span></td>
      </tr>
      <tr>
        <td id="L336" class="blob-num js-line-number" data-line-number="336"></td>
        <td id="LC336" class="blob-code blob-code-inner js-file-line">    relFreqList <span class="pl-k">=</span> [<span class="pl-c1">0.111842105</span>,<span class="pl-c1">0.059210526</span>,<span class="pl-c1">0.026315789</span>,<span class="pl-c1">0.013157895</span>,</td>
      </tr>
      <tr>
        <td id="L337" class="blob-num js-line-number" data-line-number="337"></td>
        <td id="LC337" class="blob-code blob-code-inner js-file-line">                   <span class="pl-c1">0.006578947</span>,<span class="pl-c1">0.013157895</span>,<span class="pl-c1">0.032894737</span>,<span class="pl-c1">0.019736842</span>,</td>
      </tr>
      <tr>
        <td id="L338" class="blob-num js-line-number" data-line-number="338"></td>
        <td id="LC338" class="blob-code blob-code-inner js-file-line">                   <span class="pl-c1">0.039473684</span>,<span class="pl-c1">0.046052632</span>,<span class="pl-c1">0.217105263</span>,<span class="pl-c1">0.065789474</span>,</td>
      </tr>
      <tr>
        <td id="L339" class="blob-num js-line-number" data-line-number="339"></td>
        <td id="LC339" class="blob-code blob-code-inner js-file-line">                   <span class="pl-c1">0.151315789</span>,<span class="pl-c1">0.059210526</span>,<span class="pl-c1">0.138157895</span>]</td>
      </tr>
      <tr>
        <td id="L340" class="blob-num js-line-number" data-line-number="340"></td>
        <td id="LC340" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L341" class="blob-num js-line-number" data-line-number="341"></td>
        <td id="LC341" class="blob-code blob-code-inner js-file-line">    relWeightList <span class="pl-k">=</span> [<span class="pl-c1">0.07532571</span>,<span class="pl-c1">0.05900545</span>,<span class="pl-c1">0.009601452</span>,<span class="pl-c1">0.042357532</span>,<span class="pl-c1">0.01236219</span>,<span class="pl-c1">0.001675663</span>,<span class="pl-c1">0.04109726</span>,</td>
      </tr>
      <tr>
        <td id="L342" class="blob-num js-line-number" data-line-number="342"></td>
        <td id="LC342" class="blob-code blob-code-inner js-file-line">                     <span class="pl-c1">0.097464248</span>,<span class="pl-c1">0.057491666</span>,<span class="pl-c1">0.05826875</span>,<span class="pl-c1">0.279457473</span>,<span class="pl-c1">0.070004772</span>,<span class="pl-c1">0.065329007</span>,<span class="pl-c1">0.085361298</span>,<span class="pl-c1">0.045197529</span>]</td>
      </tr>
      <tr>
        <td id="L343" class="blob-num js-line-number" data-line-number="343"></td>
        <td id="LC343" class="blob-code blob-code-inner js-file-line">
</td>
      </tr>
      <tr>
        <td id="L344" class="blob-num js-line-number" data-line-number="344"></td>
        <td id="LC344" class="blob-code blob-code-inner js-file-line">    createStackedBar(<span class="pl-s"><span class="pl-pds">&#39;</span>T_Test<span class="pl-pds">&#39;</span></span>,relWeightList, <span class="pl-s"><span class="pl-pds">&#39;</span>Tc148<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>results<span class="pl-pds">&#39;</span></span>)</td>
      </tr>
      <tr>
        <td id="L345" class="blob-num js-line-number" data-line-number="345"></td>
        <td id="LC345" class="blob-code blob-code-inner js-file-line">    createHTML(<span class="pl-s"><span class="pl-pds">&quot;</span>t_test<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>results/t_test.html<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>,relFreqList,relWeightList)</td>
      </tr>
</table>

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