Mercurial > repos > johnheap > vapper
changeset 8:e75a85590041 draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 14:09:07 -0400 |
| parents | 25226d33642e |
| children | a0d5e1f5bec0 |
| files | Tryp_V.py |
| diffstat | 1 files changed, 2064 insertions(+), 325 deletions(-) [+] |
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--- a/Tryp_V.py Mon Jun 03 14:06:47 2019 -0400 +++ b/Tryp_V.py Mon Jun 03 14:09:07 2019 -0400 @@ -1,325 +1,2064 @@ -""" - * Copyright 2018 University of Liverpool - * Author: John Heap, Computational Biology Facility, UoL - * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * - """ - -import matplotlib as mpl -mpl.use('Agg') - -import subprocess -import shutil -import re -import pandas as pd -import os - -import sys - -import matplotlib.pyplot as plt -from matplotlib.patches import Patch -import seaborn as sns - -def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name): - #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq" - argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name - print(argString) - returncode = subprocess.call(argString, shell=True) - if returncode != 0: - return "Error in velveth" - argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -clean yes -ins_length_sd 50 -min_pair_count 20" - #argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20" - #argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString - print(argString) - returncode = subprocess.call(argString, shell = True) - if returncode != 0: - return "Error in velvetg" - shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa") # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa"; - return "ok" - - -def blastContigs(test_name,database): - print(test_name) - print(database) - #db_path = os.path.dirname(os.path.realpath(__file__))+database - db_path = database - argString = "blastn -db "+db_path+" -query "+test_name+".fa -outfmt 10 -out "+test_name+"_blast.txt" - print (argString) - returncode = subprocess.call(argString, shell = True) - if returncode != 0: - return "Error in blastall" - blast_df = pd.read_csv(""+test_name+"_blast.txt") - #print (blast_df) - #if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){ - #'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore' - blast_df.columns = ['qaccver', 'saccver', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue','bitscore'] - blastResult_df = blast_df[(blast_df['pident']>=98) & (blast_df['length'] > 100) & (blast_df['evalue']<0.001) ] - blastResult_df = blastResult_df[['qaccver', 'saccver', 'pident']] #query accession.version, subject accession.version, Percentage of identical matches - - return blastResult_df - - - -def getCogsPresent(blastResult_df,strain,cogOrBinList): - blastResult_df.sort_values('pident',axis = 0, ascending=False, inplace=True) - nodeList = blastResult_df['qaccver'].tolist() - cogList = blastResult_df['saccver'].tolist() - cogSet = set(cogList) #get unique values - cogList = sorted(cogSet) #sort them - - #print (cogList) - #print (len(cogList)) - - thereList = [] - dataList = [] - #dir_path = os.path.dirname(os.path.realpath(__file__)) - fname = cogOrBinList - cnt = 0 - with open (fname) as f: - for line in f: - dataList.append(line.rstrip('\n\r ')) - if line.rstrip('\n\r ') in cogList: - thereList.append('1') - cnt = cnt+1 - else: - thereList.append('0') - - #print (thereList) - #print (cnt) - data = {'Cog': dataList, strain: thereList} - presence_df = pd.DataFrame(data) - #print (presence_df) - return presence_df - -def addToCurrentData(cog_df, name): - dir_path = os.path.dirname(os.path.realpath(__file__)) - j_fname = dir_path + r"/data/vivax/TvDatabase.csv" - tv_df = pd.read_csv(j_fname) - - cogList = cog_df[name].tolist() - #cogList.insert(0,'Test') - #print (len(tv_df)) - #print(len(cogList)) - - #print(cogList) - tv_df.loc[:,name]=cogList - return tv_df - - - - -def createClusterMap(tv_df,name,html_path,pdfExport): - #Retrieve Data - dir_path = os.path.dirname(os.path.realpath(__file__)) - j_fname = dir_path+r"/data/vivax/geoTv.csv" - geo_df = pd.read_csv(j_fname) - geo_df.loc[len(geo_df)] =[name,name,'k'] - print(geo_df) - - myStrains = tv_df.columns.values.tolist() #beware first entry is COG - myStrains = myStrains[1:] - print(myStrains) - myPal = [] - for s in myStrains: - col = geo_df[(geo_df['Strain'] == s)]['colour'].tolist() - myPal.append(col[0]) - print(myPal) - mycogmap = ['skyblue', 'orangered'] # blue absent,red present - tv_df.set_index('COG', inplace=True) - tv_df = tv_df[tv_df.columns].astype(float) - - cg = sns.clustermap(tv_df, method='ward', col_colors=myPal, cmap=mycogmap, yticklabels = 1500, row_cluster=False, linewidths = 0) - #cg = sns.clustermap(tv_df, method='ward', row_cluster=False, linewidths = 0) - ax = cg.ax_heatmap - #xasix ticks and labels. - ax.xaxis.tick_top() #set ticks at top - newlabs = [] - - labs = ax.xaxis.get_ticklabels() - for i in range(0, len(labs)): - print(labs[i]) - # labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars - newlabs.append(" " + labs[i].get_text()) - ax.xaxis.set_ticklabels(newlabs) - - #labs = ax.xaxis.get_ticklabels() - #for i in range(0, len(labs)): - # print(labs[i]) - # labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars - # print(labs[i]) - #ax.xaxis.set_ticklabels(labs) - plt.setp(cg.ax_heatmap.xaxis.get_ticklabels(), rotation=90) # get x labels printed vertically - - cg.cax.set_visible(False) - ax = cg.ax_heatmap - ax.set_yticklabels("") - ax.set_ylabel("") - ax = cg.ax_heatmap - # ax.set_title("Variant antigen profiles of T. vivax genomes.\nDendrogram reflects the VSG repertoire relationships of each strain inferred by the presence and absence of non-universal T. vivax VSG orthologs.", va = "top", wrap = "True") - b = len(tv_df) - print(b) - title = "Figure Legend: The Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ " \ - "showing the \ncombination of present and absent diagnostic cluster of VSG orthologs " \ - "across the sample cohort. \nDendrogram reflects the relationships amongst the VSG" \ - " repertoires of each strain. " \ - "Strains were isolated \nfrom multiple African countries as shown in the key.\nData was produced with the " \ - "'Variant Antigen Profiler' (Silva Pereira and Jackson, 2018)." - - ax.text(-1.5, len(tv_df) + 8, - title, - ha="left", va="top", wrap="True") - col = cg.ax_col_dendrogram.get_position() - cg.ax_col_dendrogram.set_position([col.x0, col.y0*1.08, col.width, col.height*1.1]) - - countryList = pd.unique(geo_df['Location']) - colourList = pd.unique(geo_df['colour']) - legend_elements = [Patch(facecolor='orangered', label='COG Present'), - Patch(facecolor='skyblue', label='COG Absent')] - - for i in range(0, len(colourList)): - print("country = %s, colour = %s" % (countryList[i], colourList[i])) - p = Patch(facecolor=str(colourList[i]), label=countryList[i]) - legend_elements.append(p) - - ax.legend(handles = legend_elements, bbox_to_anchor=(-0.3,1.2),loc = 'upper left') - - - - - - - - #plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0 ) # get y labels printed horizontally - # cg.dendrogram_col.linkage # linkage matrix for columns - # cg.dendrogram_row.linkage # linkage matrix for rows - # plt.savefig(r"results/" + name + "_heatmap.png") - #plt.savefig(htmlresource + "/heatmap.png") - #if pdf == 'PDF_Yes': - # plt.savefig(htmlresource + "/heatmap.pdf") - # shutil.copyfile("heatmap.pdf",heatmapfn) # - #plt.legend() - fname = html_path+"/"+name+"_clustermap.png" - cg.savefig(fname) - if pdfExport == 'PDF_Yes': - fname = html_path + "/" + name + "_clustermap.pdf" - cg.savefig(fname) - #plt.show() - -def createHTML(name,htmlfn,htmlPath): - #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource - htmlString = r"<html><title>T.vivax VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3>" - htmlString += name - - - htmlString += r'<p> <h3>The Heat Map and Dendrogram</h3></p>' - imgString = r"<img src = '"+name+"_clustermap.png' alt='Cog Clustermap' style='max-width:100%'><br><br>" - htmlString += imgString - print(htmlString) - - with open(htmlfn, "w") as htmlfile: - htmlfile.write(htmlString) - - -def vivax_assemble(args,dict): - #argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10} - #assembleWithVelvet("V2_Test", '65', '400', '5', "data/TviBrRp.1.clean", "data/TviBrRp.2.clean") - - vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax" - assembleWithVelvet(args[dict['name']], args[dict['kmers']], args[dict['inslen']], args[dict['covcut']], - args[dict['forward']], args[dict['reverse']]) - blastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/COGs.fas") - orthPresence_df = getCogsPresent(blastResult_df, args[dict['name']], vivaxPath+r"/Database/COGlist.txt") - - binBlastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/Bin_2.fas") - binPresence_df = getCogsPresent(binBlastResult_df, args[dict['name']], vivaxPath+r"/Database/binlist.txt") - cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True) - - fname = args[dict['html_resource']] +args[dict['name']]+"_cogspresent.csv" - cogPresence_df.to_csv(fname) - current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. - createClusterMap(current_df, args[dict['name']],args[dict['html_resource']],args[dict['pdfexport']]) - createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']]) - -def test_cluster(args,dict): - print ("name: %s",args[dict['name']]) - cogPresence_df = pd.read_csv("test_cogspresent.csv") - print(cogPresence_df) - current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. - createClusterMap(current_df, args[dict['name']], args[dict['html_resource']], args[dict['pdfexport']]) - -def vivax_contigs(args,dict): -# argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6} - - #test_cluster(args,dict) - #return; - - #subprocess.call('echo $PATH',shell = True) - #sys.exit(1) - - vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax" - shutil.copyfile(args[dict['contigs']], args[dict['name']]+".fa") - blastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/COGs.fas") - orthPresence_df = getCogsPresent(blastResult_df, args[dict['name']], vivaxPath+r"/Database/COGlist.txt") - - binBlastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/Bin_2.fas") - binPresence_df = getCogsPresent(binBlastResult_df, args[dict['name']], vivaxPath+r"/Database/binlist.txt") - cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True) - - fname = args[dict['html_resource']]+r"/"+ args[dict['name']]+"_cogspresent.csv" - cogPresence_df.to_csv(fname) - current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. - createClusterMap(current_df, args[dict['name']], args[dict['html_resource']], args[dict['pdfexport']]) - createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']]) - -if __name__ == "__main__": - #assembleWithVelvet("V2_Test",'65','400', '5',"data/TviBrRp.1.clean","data/TviBrRp.2.clean") - #assembleWithVelvet("V2_Test",'65','400', '5',"data/Tv493.1","data/Tv493.2") - #blastResult_df=blastContigs("V2_Test",r"/Database/COGs.fas") - cogPresence_df = pd.read_csv("test_cogspresent.csv") - print(cogPresence_df) - current_df = addToCurrentData(cogPresence_df,"vTest") # load in Tvdatabase and add cogPresence column to it. - createClusterMap(current_df, "vTest", "sausages","no") - createHTML("vTest","vTest.html","sausages") - sys.exit() - - blastResult_df=blastContigs("Tv493",r"/Database/COGs.fas") - orthPresence_df = getCogsPresent(blastResult_df,"Tv493",r"/Database/COGlist.txt") - - #binBlastResult_df=blastContigs("V2_Test",r"/Database/Bin_2.fas") - - binBlastResult_df=blastContigs("Tv493",r"/Database/Bin_2.fas") - binPresence_df = getCogsPresent(binBlastResult_df,"Tv493",r"/Database/binlist.txt") - cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True) - #now do the next bit? - current_df = addToCurrentData(cogPresence_df) # load in Tvdatabase and add cogPresence column to it. - createClusterMap(current_df,'Test',dict['html_resource'] ,dict['pdfexport']) - - - #print(cogPresence_df) - dir_path = os.path.dirname(os.path.realpath(__file__)) - fname = dir_path+r"/results/V2_TestPresence.csv" - #fnameb = dir_path+r"/results/V2_Test_blastOrth.csv" - #fnameb_bin = dir_path+r"/results/V2_Test_blastBin.csv" - #binBlastResult_df.to_csv(fnameb_bin) - #blastResult_df.to_csv(fnameb) - - #cogPresence_df.to_csv(fname) - cogPresence_df = pd.read_csv(fname) - - current_df = addToCurrentData(cogPresence_df) #load in Tvdatabase and add cogPresence column to it. 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aria-label="You must be signed in to make or propose changes"> + <svg class="octicon octicon-trashcan" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg> + </button> + </div> + </div> +</div> + + + + <div itemprop="text" class="Box-body p-0 blob-wrapper data type-python "> + +<table class="highlight tab-size js-file-line-container" data-tab-size="8"> + <tr> + <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> + <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">"""</span></span></td> + </tr> + <tr> + <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> + <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td> + </tr> + <tr> + <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> + <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author: John Heap, Computational Biology Facility, UoL</span></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the "License");</span></td> + </tr> + <tr> + <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> + <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td> + </tr> + <tr> + <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> + <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td> + </tr> + <tr> + <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> + <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> + </tr> + <tr> + <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> + <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td> + </tr> + <tr> + <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> + <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> + </tr> + <tr> + <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> + <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td> + </tr> + <tr> + <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> + <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td> + </tr> + <tr> + <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> + <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td> + </tr> + <tr> + <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> + <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td> + </tr> + <tr> + <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> + <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td> + </tr> + <tr> + <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> + <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> + </tr> + <tr> + <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> + <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td> + </tr> + <tr> + <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> + <td id="LC19" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> + <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib <span class="pl-k">as</span> mpl</td> + </tr> + <tr> + <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> + <td id="LC21" class="blob-code blob-code-inner js-file-line">mpl.use(<span class="pl-s"><span class="pl-pds">'</span>Agg<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> + <td id="LC22" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> + <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td> + </tr> + <tr> + <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> + <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td> + </tr> + <tr> + <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> + <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td> + </tr> + <tr> + <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> + <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td> + </tr> + <tr> + <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> + <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td> + </tr> + <tr> + <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> + <td id="LC28" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> + <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td> + </tr> + <tr> + <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> + <td id="LC30" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> + <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td> + </tr> + <tr> + <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> + <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">from</span> matplotlib.patches <span class="pl-k">import</span> Patch</td> + </tr> + <tr> + <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> + <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> seaborn <span class="pl-k">as</span> sns</td> + </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"> +</td> + </tr> + <tr> + <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> + <td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">assembleWithVelvet</span>(<span class="pl-smi">name</span>, <span class="pl-smi">kmers</span>, <span class="pl-smi">inslen</span>, <span class="pl-smi">covcut</span>, <span class="pl-smi">fastq1name</span>,<span class="pl-smi">fastq2name</span>):</td> + </tr> + <tr> + <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> + <td id="LC36" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"</span></td> + </tr> + <tr> + <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> + <td id="LC37" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>velveth <span class="pl-pds">"</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span> kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span><span class="pl-k">+</span> kmers <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span> -shortPaired -fastq <span class="pl-pds">"</span></span> <span class="pl-k">+</span> fastq1name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span><span class="pl-k">+</span>fastq2name</td> + </tr> + <tr> + <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> + <td id="LC38" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> + </tr> + <tr> + <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> + <td id="LC39" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> + <td id="LC40" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> + </tr> + <tr> + <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> + <td id="LC41" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in velveth<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> + <td id="LC42" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>velvetg <span class="pl-pds">"</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -exp_cov auto -ins_length <span class="pl-pds">"</span></span><span class="pl-k">+</span>inslen<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -clean yes -ins_length_sd 50 -min_pair_count 20<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> + <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"</span></td> + </tr> + <tr> + <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> + <td id="LC44" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString</span></td> + </tr> + <tr> + <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> + <td id="LC45" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> + </tr> + <tr> + <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> + <td id="LC46" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> + <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> + </tr> + <tr> + <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> + <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in velvetg<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> + <td id="LC49" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>//contigs.fa<span class="pl-pds">"</span></span>,name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.fa<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span> my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";</span></td> + </tr> + <tr> + <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> + <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>ok<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> + <td id="LC51" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> + <td id="LC52" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> + <td id="LC53" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">database</span>):</td> + </tr> + <tr> + <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> + <td id="LC54" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(test_name)</td> + </tr> + <tr> + <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> + <td id="LC55" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(database)</td> + </tr> + <tr> + <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> + <td id="LC56" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>db_path = os.path.dirname(os.path.realpath(__file__))+database</span></td> + </tr> + <tr> + <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> + <td id="LC57" class="blob-code blob-code-inner js-file-line"> db_path <span class="pl-k">=</span> database</td> + </tr> + <tr> + <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> + <td id="LC58" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>blastn -db <span class="pl-pds">"</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -query <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.fa -outfmt 10 -out <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> + <td id="LC59" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> + </tr> + <tr> + <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> + <td id="LC60" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> + <td id="LC61" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> + </tr> + <tr> + <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> + <td id="LC62" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in blastall<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> + <td id="LC63" class="blob-code blob-code-inner js-file-line"> blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> + <td id="LC64" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (blast_df)</span></td> + </tr> + <tr> + <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> + <td id="LC65" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){</span></td> + </tr> + <tr> + <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> + <td id="LC66" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore'</span></td> + </tr> + <tr> + <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> + <td id="LC67" class="blob-code blob-code-inner js-file-line"> blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>mismatch<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>gapopen<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qend<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>sstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>send<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> + <td id="LC68" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]<span class="pl-k">>=</span><span class="pl-c1">98</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">100</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>]<span class="pl-k"><</span><span class="pl-c1">0.001</span>) ]</td> + </tr> + <tr> + <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> + <td id="LC69" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]] <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td> + </tr> + <tr> + <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> + <td id="LC70" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> + <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> blastResult_df</td> + </tr> + <tr> + <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> + <td id="LC72" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> + <td id="LC73" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> + <td id="LC74" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> + <td id="LC75" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getCogsPresent</span>(<span class="pl-smi">blastResult_df</span>,<span class="pl-smi">strain</span>,<span class="pl-smi">cogOrBinList</span>):</td> + </tr> + <tr> + <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> + <td id="LC76" class="blob-code blob-code-inner js-file-line"> blastResult_df.sort_values(<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>,<span class="pl-v">axis</span> <span class="pl-k">=</span> <span class="pl-c1">0</span>, <span class="pl-v">ascending</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> + <td id="LC77" class="blob-code blob-code-inner js-file-line"> nodeList <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>].tolist()</td> + </tr> + <tr> + <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> + <td id="LC78" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>].tolist()</td> + </tr> + <tr> + <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> + <td id="LC79" class="blob-code blob-code-inner js-file-line"> cogSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(cogList) <span class="pl-c"><span class="pl-c">#</span>get unique values</span></td> + </tr> + <tr> + <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> + <td id="LC80" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> <span class="pl-c1">sorted</span>(cogSet) <span class="pl-c"><span class="pl-c">#</span>sort them</span></td> + </tr> + <tr> + <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> + <td id="LC81" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> + <td id="LC82" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (cogList)</span></td> + </tr> + <tr> + <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> + <td id="LC83" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (len(cogList))</span></td> + </tr> + <tr> + <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> + <td id="LC84" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> + <td id="LC85" class="blob-code blob-code-inner js-file-line"> thereList <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> + <td id="LC86" class="blob-code blob-code-inner js-file-line"> dataList <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> + <td id="LC87" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>dir_path = os.path.dirname(os.path.realpath(__file__))</span></td> + </tr> + <tr> + <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> + <td id="LC88" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> cogOrBinList</td> + </tr> + <tr> + <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> + <td id="LC89" class="blob-code blob-code-inner js-file-line"> cnt <span class="pl-k">=</span> <span class="pl-c1">0</span></td> + </tr> + <tr> + <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> + <td id="LC90" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span> (fname) <span class="pl-k">as</span> f:</td> + </tr> + <tr> + <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> + <td id="LC91" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> line <span class="pl-k">in</span> f:</td> + </tr> + <tr> + <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> + <td id="LC92" class="blob-code blob-code-inner js-file-line"> dataList.append(line.rstrip(<span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n\r</span> <span class="pl-pds">'</span></span>))</td> + </tr> + <tr> + <td id="L93" class="blob-num js-line-number" data-line-number="93"></td> + <td id="LC93" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line.rstrip(<span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n\r</span> <span class="pl-pds">'</span></span>) <span class="pl-k">in</span> cogList:</td> + </tr> + <tr> + <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> + <td id="LC94" class="blob-code blob-code-inner js-file-line"> thereList.append(<span class="pl-s"><span class="pl-pds">'</span>1<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L95" class="blob-num js-line-number" data-line-number="95"></td> + <td id="LC95" class="blob-code blob-code-inner js-file-line"> cnt <span class="pl-k">=</span> cnt<span class="pl-k">+</span><span class="pl-c1">1</span></td> + </tr> + <tr> + <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> + <td id="LC96" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> + </tr> + <tr> + <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> + <td id="LC97" class="blob-code blob-code-inner js-file-line"> thereList.append(<span class="pl-s"><span class="pl-pds">'</span>0<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> + <td id="LC98" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> + <td id="LC99" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (thereList)</span></td> + </tr> + <tr> + <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> + <td id="LC100" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (cnt)</span></td> + </tr> + <tr> + <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> + <td id="LC101" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>Cog<span class="pl-pds">'</span></span>: dataList, strain: thereList}</td> + </tr> + <tr> + <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> + <td id="LC102" class="blob-code blob-code-inner js-file-line"> presence_df <span class="pl-k">=</span> pd.DataFrame(data)</td> + </tr> + <tr> + <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> + <td id="LC103" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (presence_df)</span></td> + </tr> + <tr> + <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> + <td id="LC104" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> presence_df</td> + </tr> + <tr> + <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> + <td id="LC105" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> + <td id="LC106" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">addToCurrentData</span>(<span class="pl-smi">cog_df</span>, <span class="pl-smi">name</span>):</td> + </tr> + <tr> + <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> + <td id="LC107" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> + </tr> + <tr> + <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> + <td id="LC108" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax/TvDatabase<span class="pl-c1">.</span>csv<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> + <td id="LC109" class="blob-code blob-code-inner js-file-line"> tv_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td> + </tr> + <tr> + <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> + <td id="LC110" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> + <td id="LC111" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> cog_df[name].tolist()</td> + </tr> + <tr> + <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> + <td id="LC112" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cogList.insert(0,'Test')</span></td> + </tr> + <tr> + <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> + <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (len(tv_df))</span></td> + </tr> + <tr> + <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> + <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(len(cogList))</span></td> + </tr> + <tr> + <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> + <td id="LC115" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> + <td id="LC116" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(cogList)</span></td> + </tr> + <tr> + <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> + <td id="LC117" class="blob-code blob-code-inner js-file-line"> tv_df.loc[:,name]<span class="pl-k">=</span>cogList</td> + </tr> + <tr> + <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> + <td id="LC118" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> tv_df</td> + </tr> + <tr> + <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> + <td id="LC119" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L120" class="blob-num js-line-number" data-line-number="120"></td> + <td id="LC120" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> + <td id="LC121" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> + <td id="LC122" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> + <td id="LC123" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createClusterMap</span>(<span class="pl-smi">tv_df</span>,<span class="pl-smi">name</span>,<span class="pl-smi">html_path</span>,<span class="pl-smi">pdfExport</span>):</td> + </tr> + <tr> + <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> + <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>Retrieve Data</span></td> + </tr> + <tr> + <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> + <td id="LC125" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> + </tr> + <tr> + <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> + <td id="LC126" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax/geoTv<span class="pl-c1">.</span>csv<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> + <td id="LC127" class="blob-code blob-code-inner js-file-line"> geo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td> + </tr> + <tr> + <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> + <td id="LC128" class="blob-code blob-code-inner js-file-line"> geo_df.loc[<span class="pl-c1">len</span>(geo_df)] <span class="pl-k">=</span>[name,name,<span class="pl-s"><span class="pl-pds">'</span>k<span class="pl-pds">'</span></span>]</td> + </tr> + <tr> + <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> + <td id="LC129" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(geo_df)</td> + </tr> + <tr> + <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> + <td id="LC130" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> + <td id="LC131" class="blob-code blob-code-inner js-file-line"> myStrains <span class="pl-k">=</span> tv_df.columns.values.tolist() <span class="pl-c"><span class="pl-c">#</span>beware first entry is COG</span></td> + </tr> + <tr> + <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> + <td id="LC132" class="blob-code blob-code-inner js-file-line"> myStrains <span class="pl-k">=</span> myStrains[<span class="pl-c1">1</span>:]</td> + </tr> + <tr> + <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> + <td id="LC133" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(myStrains)</td> + </tr> + <tr> + <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> + <td id="LC134" class="blob-code blob-code-inner js-file-line"> myPal <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> + <td id="LC135" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> s <span class="pl-k">in</span> myStrains:</td> + </tr> + <tr> + <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> + <td id="LC136" class="blob-code blob-code-inner js-file-line"> col <span class="pl-k">=</span> geo_df[(geo_df[<span class="pl-s"><span class="pl-pds">'</span>Strain<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> s)][<span class="pl-s"><span class="pl-pds">'</span>colour<span class="pl-pds">'</span></span>].tolist()</td> + </tr> + <tr> + <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> + <td id="LC137" class="blob-code blob-code-inner js-file-line"> myPal.append(col[<span class="pl-c1">0</span>])</td> + </tr> + <tr> + <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> + <td id="LC138" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(myPal)</td> + </tr> + <tr> + <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> + <td id="LC139" class="blob-code blob-code-inner js-file-line"> mycogmap <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>skyblue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>orangered<span class="pl-pds">'</span></span>] <span class="pl-c"><span class="pl-c">#</span> blue absent,red present</span></td> + </tr> + <tr> + <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> + <td id="LC140" class="blob-code blob-code-inner js-file-line"> tv_df.set_index(<span class="pl-s"><span class="pl-pds">'</span>COG<span class="pl-pds">'</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> + <td id="LC141" class="blob-code blob-code-inner js-file-line"> tv_df <span class="pl-k">=</span> tv_df[tv_df.columns].astype(<span class="pl-c1">float</span>)</td> + </tr> + <tr> + <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> + <td id="LC142" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L143" class="blob-num js-line-number" data-line-number="143"></td> + <td id="LC143" class="blob-code blob-code-inner js-file-line"> cg <span class="pl-k">=</span> sns.clustermap(tv_df, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>ward<span class="pl-pds">'</span></span>, <span class="pl-v">col_colors</span><span class="pl-k">=</span>myPal, <span class="pl-v">cmap</span><span class="pl-k">=</span>mycogmap, <span class="pl-v">yticklabels</span> <span class="pl-k">=</span> <span class="pl-c1">1500</span>, <span class="pl-v">row_cluster</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">linewidths</span> <span class="pl-k">=</span> <span class="pl-c1">0</span>)</td> + </tr> + <tr> + <td id="L144" class="blob-num js-line-number" data-line-number="144"></td> + <td id="LC144" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cg = sns.clustermap(tv_df, method='ward', row_cluster=False, linewidths = 0)</span></td> + </tr> + <tr> + <td id="L145" class="blob-num js-line-number" data-line-number="145"></td> + <td id="LC145" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td> + </tr> + <tr> + <td id="L146" class="blob-num js-line-number" data-line-number="146"></td> + <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>xasix ticks and labels.</span></td> + </tr> + <tr> + <td id="L147" class="blob-num js-line-number" data-line-number="147"></td> + <td id="LC147" class="blob-code blob-code-inner js-file-line"> ax.xaxis.tick_top() <span class="pl-c"><span class="pl-c">#</span>set ticks at top</span></td> + </tr> + <tr> + <td id="L148" class="blob-num js-line-number" data-line-number="148"></td> + <td id="LC148" class="blob-code blob-code-inner js-file-line"> newlabs <span class="pl-k">=</span> []</td> + </tr> + <tr> + <td id="L149" class="blob-num js-line-number" data-line-number="149"></td> + <td id="LC149" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L150" class="blob-num js-line-number" data-line-number="150"></td> + <td id="LC150" class="blob-code blob-code-inner js-file-line"> labs <span class="pl-k">=</span> ax.xaxis.get_ticklabels()</td> + </tr> + <tr> + <td id="L151" class="blob-num js-line-number" data-line-number="151"></td> + <td id="LC151" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(labs)):</td> + </tr> + <tr> + <td id="L152" class="blob-num js-line-number" data-line-number="152"></td> + <td id="LC152" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(labs[i])</td> + </tr> + <tr> + <td id="L153" class="blob-num js-line-number" data-line-number="153"></td> + <td id="LC153" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars</span></td> + </tr> + <tr> + <td id="L154" class="blob-num js-line-number" data-line-number="154"></td> + <td id="LC154" class="blob-code blob-code-inner js-file-line"> newlabs.append(<span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span> <span class="pl-k">+</span> labs[i].get_text())</td> + </tr> + <tr> + <td id="L155" class="blob-num js-line-number" data-line-number="155"></td> + <td id="LC155" class="blob-code blob-code-inner js-file-line"> ax.xaxis.set_ticklabels(newlabs)</td> + </tr> + <tr> + <td id="L156" class="blob-num js-line-number" data-line-number="156"></td> + <td id="LC156" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L157" class="blob-num js-line-number" data-line-number="157"></td> + <td id="LC157" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>labs = ax.xaxis.get_ticklabels()</span></td> + </tr> + <tr> + <td id="L158" class="blob-num js-line-number" data-line-number="158"></td> + <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>for i in range(0, len(labs)):</span></td> + </tr> + <tr> + <td id="L159" class="blob-num js-line-number" data-line-number="159"></td> + <td id="LC159" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(labs[i])</span></td> + </tr> + <tr> + <td id="L160" class="blob-num js-line-number" data-line-number="160"></td> + <td id="LC160" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars</span></td> + </tr> + <tr> + <td id="L161" class="blob-num js-line-number" data-line-number="161"></td> + <td id="LC161" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(labs[i])</span></td> + </tr> + <tr> + <td id="L162" class="blob-num js-line-number" data-line-number="162"></td> + <td id="LC162" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ax.xaxis.set_ticklabels(labs)</span></td> + </tr> + <tr> + <td id="L163" class="blob-num js-line-number" data-line-number="163"></td> + <td id="LC163" class="blob-code blob-code-inner js-file-line"> plt.setp(cg.ax_heatmap.xaxis.get_ticklabels(), <span class="pl-v">rotation</span><span class="pl-k">=</span><span class="pl-c1">90</span>) <span class="pl-c"><span class="pl-c">#</span> get x labels printed vertically</span></td> + </tr> + <tr> + <td id="L164" class="blob-num js-line-number" data-line-number="164"></td> + <td id="LC164" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L165" class="blob-num js-line-number" data-line-number="165"></td> + <td id="LC165" class="blob-code blob-code-inner js-file-line"> cg.cax.set_visible(<span class="pl-c1">False</span>)</td> + </tr> + <tr> + <td id="L166" class="blob-num js-line-number" data-line-number="166"></td> + <td id="LC166" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td> + </tr> + <tr> + <td id="L167" class="blob-num js-line-number" data-line-number="167"></td> + <td id="LC167" class="blob-code blob-code-inner js-file-line"> ax.set_yticklabels(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L168" class="blob-num js-line-number" data-line-number="168"></td> + <td id="LC168" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L169" class="blob-num js-line-number" data-line-number="169"></td> + <td id="LC169" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td> + </tr> + <tr> + <td id="L170" class="blob-num js-line-number" data-line-number="170"></td> + <td id="LC170" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> ax.set_title("Variant antigen profiles of T. vivax genomes.\nDendrogram reflects the VSG repertoire relationships of each strain inferred by the presence and absence of non-universal T. vivax VSG orthologs.", va = "top", wrap = "True")</span></td> + </tr> + <tr> + <td id="L171" class="blob-num js-line-number" data-line-number="171"></td> + <td id="LC171" class="blob-code blob-code-inner js-file-line"> b <span class="pl-k">=</span> <span class="pl-c1">len</span>(tv_df)</td> + </tr> + <tr> + <td id="L172" class="blob-num js-line-number" data-line-number="172"></td> + <td id="LC172" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(b)</td> + </tr> + <tr> + <td id="L173" class="blob-num js-line-number" data-line-number="173"></td> + <td id="LC173" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Figure Legend: The Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L174" class="blob-num js-line-number" data-line-number="174"></td> + <td id="LC174" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>showing the <span class="pl-cce">\n</span>combination of present and absent diagnostic cluster of VSG orthologs <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L175" class="blob-num js-line-number" data-line-number="175"></td> + <td id="LC175" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>across the sample cohort. <span class="pl-cce">\n</span>Dendrogram reflects the relationships amongst the VSG<span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L176" class="blob-num js-line-number" data-line-number="176"></td> + <td id="LC176" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span> repertoires of each strain. <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L177" class="blob-num js-line-number" data-line-number="177"></td> + <td id="LC177" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Strains were isolated <span class="pl-cce">\n</span>from multiple African countries as shown in the key.<span class="pl-cce">\n</span>Data was produced with the <span class="pl-pds">"</span></span> \</td> + </tr> + <tr> + <td id="L178" class="blob-num js-line-number" data-line-number="178"></td> + <td id="LC178" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>'Variant Antigen Profiler' (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L179" class="blob-num js-line-number" data-line-number="179"></td> + <td id="LC179" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L180" class="blob-num js-line-number" data-line-number="180"></td> + <td id="LC180" class="blob-code blob-code-inner js-file-line"> ax.text(<span class="pl-k">-</span><span class="pl-c1">1.5</span>, <span class="pl-c1">len</span>(tv_df) <span class="pl-k">+</span> <span class="pl-c1">8</span>,</td> + </tr> + <tr> + <td id="L181" class="blob-num js-line-number" data-line-number="181"></td> + <td id="LC181" class="blob-code blob-code-inner js-file-line"> title,</td> + </tr> + <tr> + <td id="L182" class="blob-num js-line-number" data-line-number="182"></td> + <td id="LC182" class="blob-code blob-code-inner js-file-line"> <span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>left<span class="pl-pds">"</span></span>, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>top<span class="pl-pds">"</span></span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>True<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L183" class="blob-num js-line-number" data-line-number="183"></td> + <td id="LC183" class="blob-code blob-code-inner js-file-line"> col <span class="pl-k">=</span> cg.ax_col_dendrogram.get_position()</td> + </tr> + <tr> + <td id="L184" class="blob-num js-line-number" data-line-number="184"></td> + <td id="LC184" class="blob-code blob-code-inner js-file-line"> cg.ax_col_dendrogram.set_position([col.x0, col.y0<span class="pl-k">*</span><span class="pl-c1">1.08</span>, col.width, col.height<span class="pl-k">*</span><span class="pl-c1">1.1</span>])</td> + </tr> + <tr> + <td id="L185" class="blob-num js-line-number" data-line-number="185"></td> + <td id="LC185" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L186" class="blob-num js-line-number" data-line-number="186"></td> + <td id="LC186" class="blob-code blob-code-inner js-file-line"> countryList <span class="pl-k">=</span> pd.unique(geo_df[<span class="pl-s"><span class="pl-pds">'</span>Location<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L187" class="blob-num js-line-number" data-line-number="187"></td> + <td id="LC187" class="blob-code blob-code-inner js-file-line"> colourList <span class="pl-k">=</span> pd.unique(geo_df[<span class="pl-s"><span class="pl-pds">'</span>colour<span class="pl-pds">'</span></span>])</td> + </tr> + <tr> + <td id="L188" class="blob-num js-line-number" data-line-number="188"></td> + <td id="LC188" class="blob-code blob-code-inner js-file-line"> legend_elements <span class="pl-k">=</span> [Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>orangered<span class="pl-pds">'</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>COG Present<span class="pl-pds">'</span></span>),</td> + </tr> + <tr> + <td id="L189" class="blob-num js-line-number" data-line-number="189"></td> + <td id="LC189" class="blob-code blob-code-inner js-file-line"> Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>skyblue<span class="pl-pds">'</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>COG Absent<span class="pl-pds">'</span></span>)]</td> + </tr> + <tr> + <td id="L190" class="blob-num js-line-number" data-line-number="190"></td> + <td id="LC190" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L191" class="blob-num js-line-number" data-line-number="191"></td> + <td id="LC191" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(colourList)):</td> + </tr> + <tr> + <td id="L192" class="blob-num js-line-number" data-line-number="192"></td> + <td id="LC192" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>country = <span class="pl-c1">%s</span>, colour = <span class="pl-c1">%s</span><span class="pl-pds">"</span></span> <span class="pl-k">%</span> (countryList[i], colourList[i]))</td> + </tr> + <tr> + <td id="L193" class="blob-num js-line-number" data-line-number="193"></td> + <td id="LC193" class="blob-code blob-code-inner js-file-line"> p <span class="pl-k">=</span> Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-c1">str</span>(colourList[i]), <span class="pl-v">label</span><span class="pl-k">=</span>countryList[i])</td> + </tr> + <tr> + <td id="L194" class="blob-num js-line-number" data-line-number="194"></td> + <td id="LC194" class="blob-code blob-code-inner js-file-line"> legend_elements.append(p)</td> + </tr> + <tr> + <td id="L195" class="blob-num js-line-number" data-line-number="195"></td> + <td id="LC195" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L196" class="blob-num js-line-number" data-line-number="196"></td> + <td id="LC196" class="blob-code blob-code-inner js-file-line"> ax.legend(<span class="pl-v">handles</span> <span class="pl-k">=</span> legend_elements, <span class="pl-v">bbox_to_anchor</span><span class="pl-k">=</span>(<span class="pl-k">-</span><span class="pl-c1">0.3</span>,<span class="pl-c1">1.2</span>),<span class="pl-v">loc</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>upper left<span class="pl-pds">'</span></span>)</td> + </tr> + <tr> + <td id="L197" class="blob-num js-line-number" data-line-number="197"></td> + <td id="LC197" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L198" class="blob-num js-line-number" data-line-number="198"></td> + <td id="LC198" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L199" class="blob-num js-line-number" data-line-number="199"></td> + <td id="LC199" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L200" class="blob-num js-line-number" data-line-number="200"></td> + <td id="LC200" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L201" class="blob-num js-line-number" data-line-number="201"></td> + <td id="LC201" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L202" class="blob-num js-line-number" data-line-number="202"></td> + <td id="LC202" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L203" class="blob-num js-line-number" data-line-number="203"></td> + <td id="LC203" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L204" class="blob-num js-line-number" data-line-number="204"></td> + <td id="LC204" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0 ) # get y labels printed horizontally</span></td> + </tr> + <tr> + <td id="L205" class="blob-num js-line-number" data-line-number="205"></td> + <td id="LC205" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_col.linkage # linkage matrix for columns</span></td> + </tr> + <tr> + <td id="L206" class="blob-num js-line-number" data-line-number="206"></td> + <td id="LC206" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_row.linkage # linkage matrix for rows</span></td> + </tr> + <tr> + <td id="L207" class="blob-num js-line-number" data-line-number="207"></td> + <td id="LC207" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.savefig(r"results/" + name + "_heatmap.png")</span></td> + </tr> + <tr> + <td id="L208" class="blob-num js-line-number" data-line-number="208"></td> + <td id="LC208" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.savefig(htmlresource + "/heatmap.png")</span></td> + </tr> + <tr> + <td id="L209" class="blob-num js-line-number" data-line-number="209"></td> + <td id="LC209" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>if pdf == 'PDF_Yes':</span></td> + </tr> + <tr> + <td id="L210" class="blob-num js-line-number" data-line-number="210"></td> + <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.savefig(htmlresource + "/heatmap.pdf")</span></td> + </tr> + <tr> + <td id="L211" class="blob-num js-line-number" data-line-number="211"></td> + <td id="LC211" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> shutil.copyfile("heatmap.pdf",heatmapfn) #</span></td> + </tr> + <tr> + <td id="L212" class="blob-num js-line-number" data-line-number="212"></td> + <td id="LC212" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.legend()</span></td> + </tr> + <tr> + <td id="L213" class="blob-num js-line-number" data-line-number="213"></td> + <td id="LC213" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> html_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_clustermap.png<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L214" class="blob-num js-line-number" data-line-number="214"></td> + <td id="LC214" class="blob-code blob-code-inner js-file-line"> cg.savefig(fname)</td> + </tr> + <tr> + <td id="L215" class="blob-num js-line-number" data-line-number="215"></td> + <td id="LC215" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> pdfExport <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td> + </tr> + <tr> + <td id="L216" class="blob-num js-line-number" data-line-number="216"></td> + <td id="LC216" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> html_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_clustermap.pdf<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L217" class="blob-num js-line-number" data-line-number="217"></td> + <td id="LC217" class="blob-code blob-code-inner js-file-line"> cg.savefig(fname)</td> + </tr> + <tr> + <td id="L218" class="blob-num js-line-number" data-line-number="218"></td> + <td id="LC218" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td> + </tr> + <tr> + <td id="L219" class="blob-num js-line-number" data-line-number="219"></td> + <td id="LC219" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L220" class="blob-num js-line-number" data-line-number="220"></td> + <td id="LC220" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">name</span>,<span class="pl-smi">htmlfn</span>,<span class="pl-smi">htmlPath</span>):</td> + </tr> + <tr> + <td id="L221" class="blob-num js-line-number" data-line-number="221"></td> + <td id="LC221" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td> + </tr> + <tr> + <td id="L222" class="blob-num js-line-number" data-line-number="222"></td> + <td id="LC222" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L223" class="blob-num js-line-number" data-line-number="223"></td> + <td id="LC223" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> name</td> + </tr> + <tr> + <td id="L224" class="blob-num js-line-number" data-line-number="224"></td> + <td id="LC224" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L225" class="blob-num js-line-number" data-line-number="225"></td> + <td id="LC225" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L226" class="blob-num js-line-number" data-line-number="226"></td> + <td id="LC226" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">'</span><p> <h3>The Heat Map and Dendrogram</h3></p><span class="pl-pds">'</span></span></td> + </tr> + <tr> + <td id="L227" class="blob-num js-line-number" data-line-number="227"></td> + <td id="LC227" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_clustermap.png' alt='Cog Clustermap' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L228" class="blob-num js-line-number" data-line-number="228"></td> + <td id="LC228" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> + </tr> + <tr> + <td id="L229" class="blob-num js-line-number" data-line-number="229"></td> + <td id="LC229" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(htmlString)</td> + </tr> + <tr> + <td id="L230" class="blob-num js-line-number" data-line-number="230"></td> + <td id="LC230" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L231" class="blob-num js-line-number" data-line-number="231"></td> + <td id="LC231" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(htmlfn, <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td> + </tr> + <tr> + <td id="L232" class="blob-num js-line-number" data-line-number="232"></td> + <td id="LC232" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> + </tr> + <tr> + <td id="L233" class="blob-num js-line-number" data-line-number="233"></td> + <td id="LC233" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L234" class="blob-num js-line-number" data-line-number="234"></td> + <td id="LC234" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L235" class="blob-num js-line-number" data-line-number="235"></td> + <td id="LC235" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">vivax_assemble</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td> + </tr> + <tr> + <td id="L236" class="blob-num js-line-number" data-line-number="236"></td> + <td id="LC236" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10}</span></td> + </tr> + <tr> + <td id="L237" class="blob-num js-line-number" data-line-number="237"></td> + <td id="LC237" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assembleWithVelvet("V2_Test", '65', '400', '5', "data/TviBrRp.1.clean", "data/TviBrRp.2.clean")</span></td> + </tr> + <tr> + <td id="L238" class="blob-num js-line-number" data-line-number="238"></td> + <td id="LC238" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L239" class="blob-num js-line-number" data-line-number="239"></td> + <td id="LC239" class="blob-code blob-code-inner js-file-line"> vivaxPath <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L240" class="blob-num js-line-number" data-line-number="240"></td> + <td id="LC240" class="blob-code blob-code-inner js-file-line"> assembleWithVelvet(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>kmers<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>]],</td> + </tr> + <tr> + <td id="L241" class="blob-num js-line-number" data-line-number="241"></td> + <td id="LC241" class="blob-code blob-code-inner js-file-line"> args[dict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]])</td> + </tr> + <tr> + <td id="L242" class="blob-num js-line-number" data-line-number="242"></td> + <td id="LC242" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L243" class="blob-num js-line-number" data-line-number="243"></td> + <td id="LC243" class="blob-code blob-code-inner js-file-line"> orthPresence_df <span class="pl-k">=</span> getCogsPresent(blastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L244" class="blob-num js-line-number" data-line-number="244"></td> + <td id="LC244" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L245" class="blob-num js-line-number" data-line-number="245"></td> + <td id="LC245" class="blob-code blob-code-inner js-file-line"> binBlastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L246" class="blob-num js-line-number" data-line-number="246"></td> + <td id="LC246" class="blob-code blob-code-inner js-file-line"> binPresence_df <span class="pl-k">=</span> getCogsPresent(binBlastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L247" class="blob-num js-line-number" data-line-number="247"></td> + <td id="LC247" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> orthPresence_df.append(binPresence_df, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L248" class="blob-num js-line-number" data-line-number="248"></td> + <td id="LC248" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L249" class="blob-num js-line-number" data-line-number="249"></td> + <td id="LC249" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]] <span class="pl-k">+</span>args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_cogspresent.csv<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L250" class="blob-num js-line-number" data-line-number="250"></td> + <td id="LC250" class="blob-code blob-code-inner js-file-line"> cogPresence_df.to_csv(fname)</td> + </tr> + <tr> + <td id="L251" class="blob-num js-line-number" data-line-number="251"></td> + <td id="LC251" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td> + </tr> + <tr> + <td id="L252" class="blob-num js-line-number" data-line-number="252"></td> + <td id="LC252" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td> + </tr> + <tr> + <td id="L253" class="blob-num js-line-number" data-line-number="253"></td> + <td id="LC253" class="blob-code blob-code-inner js-file-line"> createHTML(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]])</td> + </tr> + <tr> + <td id="L254" class="blob-num js-line-number" data-line-number="254"></td> + <td id="LC254" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L255" class="blob-num js-line-number" data-line-number="255"></td> + <td id="LC255" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">test_cluster</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td> + </tr> + <tr> + <td id="L256" class="blob-num js-line-number" data-line-number="256"></td> + <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span> (<span class="pl-s"><span class="pl-pds">"</span>name: <span class="pl-c1">%s</span><span class="pl-pds">"</span></span>,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]])</td> + </tr> + <tr> + <td id="L257" class="blob-num js-line-number" data-line-number="257"></td> + <td id="LC257" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span>test_cogspresent.csv<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L258" class="blob-num js-line-number" data-line-number="258"></td> + <td id="LC258" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(cogPresence_df)</td> + </tr> + <tr> + <td id="L259" class="blob-num js-line-number" data-line-number="259"></td> + <td id="LC259" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td> + </tr> + <tr> + <td id="L260" class="blob-num js-line-number" data-line-number="260"></td> + <td id="LC260" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td> + </tr> + <tr> + <td id="L261" class="blob-num js-line-number" data-line-number="261"></td> + <td id="LC261" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L262" class="blob-num js-line-number" data-line-number="262"></td> + <td id="LC262" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">vivax_contigs</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td> + </tr> + <tr> + <td id="L263" class="blob-num js-line-number" data-line-number="263"></td> + <td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6}</span></td> + </tr> + <tr> + <td id="L264" class="blob-num js-line-number" data-line-number="264"></td> + <td id="LC264" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L265" class="blob-num js-line-number" data-line-number="265"></td> + <td id="LC265" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>test_cluster(args,dict)</span></td> + </tr> + <tr> + <td id="L266" class="blob-num js-line-number" data-line-number="266"></td> + <td id="LC266" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>return;</span></td> + </tr> + <tr> + <td id="L267" class="blob-num js-line-number" data-line-number="267"></td> + <td id="LC267" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L268" class="blob-num js-line-number" data-line-number="268"></td> + <td id="LC268" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>subprocess.call('echo $PATH',shell = True)</span></td> + </tr> + <tr> + <td id="L269" class="blob-num js-line-number" data-line-number="269"></td> + <td id="LC269" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>sys.exit(1)</span></td> + </tr> + <tr> + <td id="L270" class="blob-num js-line-number" data-line-number="270"></td> + <td id="LC270" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L271" class="blob-num js-line-number" data-line-number="271"></td> + <td id="LC271" class="blob-code blob-code-inner js-file-line"> vivaxPath <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L272" class="blob-num js-line-number" data-line-number="272"></td> + <td id="LC272" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(args[dict[<span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.fa<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L273" class="blob-num js-line-number" data-line-number="273"></td> + <td id="LC273" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L274" class="blob-num js-line-number" data-line-number="274"></td> + <td id="LC274" class="blob-code blob-code-inner js-file-line"> orthPresence_df <span class="pl-k">=</span> getCogsPresent(blastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L275" class="blob-num js-line-number" data-line-number="275"></td> + <td id="LC275" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L276" class="blob-num js-line-number" data-line-number="276"></td> + <td id="LC276" class="blob-code blob-code-inner js-file-line"> binBlastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L277" class="blob-num js-line-number" data-line-number="277"></td> + <td id="LC277" class="blob-code blob-code-inner js-file-line"> binPresence_df <span class="pl-k">=</span> getCogsPresent(binBlastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td> + </tr> + <tr> + <td id="L278" class="blob-num js-line-number" data-line-number="278"></td> + <td id="LC278" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> orthPresence_df.append(binPresence_df, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> + </tr> + <tr> + <td id="L279" class="blob-num js-line-number" data-line-number="279"></td> + <td id="LC279" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L280" class="blob-num js-line-number" data-line-number="280"></td> + <td id="LC280" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_cogspresent.csv<span class="pl-pds">"</span></span></td> + </tr> + <tr> + <td id="L281" class="blob-num js-line-number" data-line-number="281"></td> + <td id="LC281" class="blob-code blob-code-inner js-file-line"> cogPresence_df.to_csv(fname)</td> + </tr> + <tr> + <td id="L282" class="blob-num js-line-number" data-line-number="282"></td> + <td id="LC282" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span> load in Tvdatabase and add cogPresence column to it.</span></td> + </tr> + <tr> + <td id="L283" class="blob-num js-line-number" data-line-number="283"></td> + <td id="LC283" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td> + </tr> + <tr> + <td id="L284" class="blob-num js-line-number" data-line-number="284"></td> + <td id="LC284" class="blob-code blob-code-inner js-file-line"> createHTML(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]])</td> + </tr> + <tr> + <td id="L285" class="blob-num js-line-number" data-line-number="285"></td> + <td id="LC285" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L286" class="blob-num js-line-number" data-line-number="286"></td> + <td id="LC286" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L287" class="blob-num js-line-number" data-line-number="287"></td> + <td id="LC287" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>__main__<span class="pl-pds">"</span></span>:</td> + </tr> + <tr> + <td id="L288" class="blob-num js-line-number" data-line-number="288"></td> + <td id="LC288" class="blob-code blob-code-inner js-file-line"> sys.exit()</td> + </tr> + <tr> + <td id="L289" class="blob-num js-line-number" data-line-number="289"></td> + <td id="LC289" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L290" class="blob-num js-line-number" data-line-number="290"></td> + <td id="LC290" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + 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