Mercurial > repos > johnheap > vapper
changeset 17:5e346d75ccf3 draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 15:59:39 -0400 |
| parents | c4e87b277576 |
| children | e7da2274c9f6 |
| files | Tryp_T.py |
| diffstat | 1 files changed, 309 insertions(+), 2225 deletions(-) [+] |
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<li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> - </ul> - </div> - </details> - </li> - </ul> - </nav> +import subprocess +import pandas as pd +import re +import os +import sys +import matplotlib as mpl +mpl.use('Agg') +import matplotlib.pyplot as plt - <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left"> - <div class="d-lg-flex mb-3 mb-lg-0"> - <div class="header-search flex-self-stretch flex-lg-self-auto mr-0 mr-lg-3 mb-3 mb-lg-0 scoped-search site-scoped-search js-site-search position-relative js-jump-to" - role="combobox" - aria-owns="jump-to-results" - aria-label="Search or jump to" - aria-haspopup="listbox" - aria-expanded="false" -> - <div class="position-relative"> - <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="139730674" data-scoped-search-url="/johnheap/VAPPER-Galaxy/search" data-unscoped-search-url="/search" action="/johnheap/VAPPER-Galaxy/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> - <label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container"> - <input type="text" - class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable" - data-hotkey="s,/" - name="q" - value="" - placeholder="Search" - data-unscoped-placeholder="Search GitHub" - data-scoped-placeholder="Search" - autocapitalize="off" - aria-autocomplete="list" - aria-controls="jump-to-results" - aria-label="Search" - data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=aIF6VlsMjmBGKiH9gFW0N7Dd6tKGBfaVG4YIMScDT9WHVDbYUTh6gnqmb9yMT8saP+1TzsRaVWx++i39m514Bw==" - spellcheck="false" - autocomplete="off" - > - <input type="hidden" class="js-site-search-type-field" name="type" > - <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> - - <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> - -<ul class="d-none js-jump-to-suggestions-template-container"> - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - -</ul> +pList = ['P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'P9', 'P10', 'P11', 'P12', 'P13', 'P14', 'P15'] +quietString = "" #"">> Vap_log.txt 2>&1" +def transcriptMapping(inputname, strain, forwardFN,reverseFN): + #where is our Reference data - + dir_path = os.path.dirname(os.path.realpath(__file__)) + refName = dir_path+"/data/Reference/Tc148" #default + if strain == "Tc148": + refName = dir_path+"/data/Reference/Tc148" + if strain == "IL3000": + refName = dir_path+"/data/Reference/IL3000" + #argString = "bowtie2 -x Refe4rence/IL3000 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt + #argString = "bowtie2 -x Reference/Tc148 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt + argString = "bowtie2 -x "+refName+" -1 "+forwardFN+" -2 "+reverseFN+" -S "+inputname+".sam"+quietString #>log.txt + #print(argString) + returncode = subprocess.call(argString, shell=True) -<ul class="d-none js-jump-to-no-results-template-container"> - <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> - <span class="text-gray">No suggested jump to results</span> - </li> -</ul> - -<ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container"> - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> +def processSamFiles(inputname): + #debug use a mapping sam file we have already found + #dir_path = os.path.dirname(os.path.realpath(__file__)) + #bugName = dir_path+"/data/T_Test" #defasult - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> - <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> - <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + cur_path = os.getcwd() + samName = cur_path+"/"+inputname - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> + #argString = "samtools view -bS "+bugName+" > "+inputname+".bam" + argString = "samtools view -bS "+inputname+".sam > "+samName+".bam"+quietString + #print(argString) + returncode = subprocess.call(argString, shell=True) -</ul> - - </div> - </label> -</form> </div> -</div> - - </div> - - <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"A68B:03C7:99543:10DBF9:5CF561B6","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="ee13ebea83318ac27e6a65b780a208b4ce93890e3887689f786a3a86a3aa41cb" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FTryp_T.py"> - 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346 lines (301 sloc) - <span class="file-info-divider"></span> - 15 KB - </div> - - <div class="d-flex py-1 py-md-0 flex-auto flex-order-1 flex-md-order-2 flex-sm-grow-0 flex-justify-between"> - - <div class="BtnGroup"> - <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/raw/master/Tryp_T.py">Raw</a> - <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/johnheap/VAPPER-Galaxy/blame/master/Tryp_T.py">Blame</a> - <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/Tryp_T.py">History</a> - </div> +def transcriptAbundance(inputname, strain): + dir_path = os.path.dirname(os.path.realpath(__file__)) + refName = dir_path + "/data/Reference/ORFAnnotation.gtf" # defasult + if strain == "Tc148": + refName = dir_path + "/data/Reference/ORFAnnotation.gtf" + if strain == "IL3000": + refName = dir_path + "/data/Reference/IL3000.gtf" + #argString = "cufflinks -G Reference/IL3000.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted" + #argString = "cufflinks -G Reference/ORFAnnotation.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted" + argString = "cufflinks -q -G "+refName+" -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"+quietString + returncode = subprocess.call(argString, shell = True) - <div> +def convertToFasta(inputName, strain): #equivalent to Sara's awk scripte + dir_path = os.path.dirname(os.path.realpath(__file__)) + refName = dir_path + "/data/Reference/ORFAnnotation.gtf" # default + if strain == "Tc148": + refName = dir_path + "/data/Reference/148_prot.fasta" + if strain == "IL3000": + refName = dir_path + "/data/Reference/IL3000_prot.fasta" + + cuff_df = pd.read_csv(inputName+".cuff/genes.fpkm_tracking", sep='\t') + cuff_df = cuff_df[(cuff_df['FPKM'] > 0)] + cuff_df.to_csv("cuffTest.csv") + gene_id_List = cuff_df['gene_id'].tolist() + + #print(gene_id_List) + #print ("Found from 8880="+str(found)) - <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw" - aria-label="You must be signed in to make or propose changes"> - <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg> - </button> - <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw" - 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> - - + # need to load in IL3000_prot.fasta + # for each line with >TcIL3000_1_1940 + # search within cuff_df[gene_id] for match + # add it to the outfile. (need to save it as used by hmmer later + number = 0 + all = 0 + with open(inputName+"_6frame.fas", 'w') as outfile: + ref = open(refName,'r') + #ref = open(r"Reference/IL3000_prot.fasta",'r') + n = 0 + line = ref.readline() + while line: + if line[0] == '>': + all = all+1 + ln = line[1:] #remove > + ln = ln.rstrip() #remove /n /r etc + #print (ln) + if ln in gene_id_List: + number = number+1 + outfile.write(line) + line = ref.readline() + if line: + while line[0] != '>': + outfile.write(line) + line=ref.readline() + if not line: + break; + else: + line = ref.readline() + else: + line =ref.readline() + ref.close() + print(str(len(gene_id_List))+":"+str(number)+" from "+str(all)) + return cuff_df - <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"> -</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"><span class="pl-k">import</span> subprocess</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"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</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> re</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> os</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> sys</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> matplotlib <span class="pl-k">as</span> mpl</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">mpl.use(<span class="pl-s"><span class="pl-pds">'</span>Agg<span class="pl-pds">'</span></span>)</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"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</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"> -</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">pList <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>P1<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P2<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P3<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P4<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P5<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P6<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P7<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P8<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P9<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P10<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P11<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P12<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P13<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P14<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>P15<span class="pl-pds">'</span></span>]</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">quietString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span>"">> Vap_log.txt 2>&1"</span></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">def</span> <span class="pl-en">transcriptMapping</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">strain</span>, <span class="pl-smi">forwardFN</span>,<span class="pl-smi">reverseFN</span>):</td> - </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-c"><span class="pl-c">#</span>where is our Reference data -</span></td> - </tr> - <tr> - <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> - <td id="LC34" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> - </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"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/data/Reference/Tc148<span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span>default</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-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> - <td id="LC37" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/data/Reference/Tc148<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> - <td id="LC38" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> - <td id="LC39" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/data/Reference/IL3000<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> - <td id="LC40" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "bowtie2 -x Refe4rence/IL3000 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt</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-c"><span class="pl-c">#</span>argString = "bowtie2 -x Reference/Tc148 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt</span></td> - </tr> - <tr> - <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> - <td id="LC42" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2 -x <span class="pl-pds">"</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -1 <span class="pl-pds">"</span></span><span class="pl-k">+</span>forwardFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -2 <span class="pl-pds">"</span></span><span class="pl-k">+</span>reverseFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -S <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam<span class="pl-pds">"</span></span><span class="pl-k">+</span>quietString <span class="pl-c"><span class="pl-c">#</span>>log.txt</span></td> - </tr> - <tr> - <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> - <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(argString)</span></td> - </tr> - <tr> - <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> - <td id="LC44" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> - <td id="LC45" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> - <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">processSamFiles</span>(<span class="pl-smi">inputname</span>):</td> - </tr> - <tr> - <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> - <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>debug use a mapping sam file we have already found</span></td> - </tr> - <tr> - <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> - <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>dir_path = os.path.dirname(os.path.realpath(__file__))</span></td> - </tr> - <tr> - <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> - <td id="LC49" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>bugName = dir_path+"/data/T_Test" #defasult</span></td> - </tr> - <tr> - <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> - <td id="LC50" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> - <td id="LC51" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td> - </tr> - <tr> - <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> - <td id="LC52" class="blob-code blob-code-inner js-file-line"> samName <span class="pl-k">=</span> cur_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname</td> - </tr> - <tr> - <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> - <td id="LC53" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> - <td id="LC54" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "samtools view -bS "+bugName+" > "+inputname+".bam"</span></td> - </tr> - <tr> - <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> - <td id="LC55" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools view -bS <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam > <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span><span class="pl-k">+</span>quietString</td> - </tr> - <tr> - <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> - <td id="LC56" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(argString)</span></td> - </tr> - <tr> - <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> - <td id="LC57" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> - <td id="LC58" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> - <td id="LC59" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> - <td id="LC60" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "samtools sort "+bugName+" -o "+inputname+".sorted"</span></td> - </tr> - <tr> - <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> - <td id="LC61" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools sort <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span><span class="pl-k">+</span>quietString</td> - </tr> - <tr> - <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> - <td id="LC62" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("argstring = "+argString)</span></td> - </tr> - <tr> - <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> - <td id="LC63" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> - <td id="LC64" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> - <td id="LC65" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "samtools index "+bugName+".sorted "+inputname+".sorted.bai"</span></td> - </tr> - <tr> - <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> - <td id="LC66" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools index <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span><span class="pl-k">+</span>quietString</td> - </tr> - <tr> - <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> - <td id="LC67" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("argstring = " + argString)</span></td> - </tr> - <tr> - <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> - <td id="LC68" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> - <td id="LC69" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> - <td id="LC70" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> - <td id="LC71" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> - <td id="LC72" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> - <td id="LC73" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptAbundance</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">strain</span>):</td> - </tr> - <tr> - <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> - <td id="LC74" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> - </tr> - <tr> - <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> - <td id="LC75" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span> defasult</span></td> - </tr> - <tr> - <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> - <td id="LC76" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> - <td id="LC77" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> - <td id="LC78" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> - <td id="LC79" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/IL3000.gtf<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> - <td id="LC80" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "cufflinks -G Reference/IL3000.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"</span></td> - </tr> - <tr> - <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> - <td id="LC81" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "cufflinks -G Reference/ORFAnnotation.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"</span></td> - </tr> - <tr> - <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> - <td id="LC82" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>cufflinks -q -G <span class="pl-pds">"</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.cuff -u -p 8 <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span><span class="pl-k">+</span>quietString</td> - </tr> - <tr> - <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> - <td id="LC83" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> - <td id="LC84" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> - <td id="LC85" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> - <td id="LC86" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">convertToFasta</span>(<span class="pl-smi">inputName</span>, <span class="pl-smi">strain</span>): <span class="pl-c"><span class="pl-c">#</span>equivalent to Sara's awk scripte</span></td> - </tr> - <tr> - <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> - <td id="LC87" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> - </tr> - <tr> - <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> - <td id="LC88" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">"</span></span> <span class="pl-c"><span class="pl-c">#</span> default</span></td> - </tr> - <tr> - <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> - <td id="LC89" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> - <td id="LC90" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/148_prot.fasta<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> - <td id="LC91" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> - <td id="LC92" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/IL3000_prot.fasta<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"> -</td> - </tr> - <tr> - <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> - <td id="LC94" class="blob-code blob-code-inner js-file-line"> cuff_df <span class="pl-k">=</span> pd.read_csv(inputName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.cuff/genes.fpkm_tracking<span class="pl-pds">"</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><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"> cuff_df <span class="pl-k">=</span> cuff_df[(cuff_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">0</span>)]</td> - </tr> - <tr> - <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> - <td id="LC96" class="blob-code blob-code-inner js-file-line"> cuff_df.to_csv(<span class="pl-s"><span class="pl-pds">"</span>cuffTest.csv<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> - <td id="LC97" class="blob-code blob-code-inner js-file-line"> gene_id_List <span class="pl-k">=</span> cuff_df[<span class="pl-s"><span class="pl-pds">'</span>gene_id<span class="pl-pds">'</span></span>].tolist()</td> - </tr> - <tr> - <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> - <td id="LC98" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> - <td id="LC99" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(gene_id_List)</span></td> - </tr> - <tr> - <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> - <td id="LC100" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print ("Found from 8880="+str(found))</span></td> - </tr> - <tr> - <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> - <td id="LC101" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> - <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> need to load in IL3000_prot.fasta</span></td> - </tr> - <tr> - <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> - <td id="LC103" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> for each line with >TcIL3000_1_1940</span></td> - </tr> - <tr> - <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> - <td id="LC104" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> search within cuff_df[gene_id] for match</span></td> - </tr> - <tr> - <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> - <td id="LC105" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> add it to the outfile. (need to save it as used by hmmer later</span></td> - </tr> - <tr> - <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> - <td id="LC106" class="blob-code blob-code-inner js-file-line"> number <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> - <td id="LC107" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">all</span> <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> - <td id="LC108" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(inputName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_6frame.fas<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> outfile:</td> - </tr> - <tr> - <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> - <td id="LC109" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> <span class="pl-c1">open</span>(refName,<span class="pl-s"><span class="pl-pds">'</span>r<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> - <td id="LC110" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ref = open(r"Reference/IL3000_prot.fasta",'r')</span></td> - </tr> - <tr> - <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> - <td id="LC111" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> - <td id="LC112" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td> - </tr> - <tr> - <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> - <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">while</span> line:</td> - </tr> - <tr> - <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> - <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line[<span class="pl-c1">0</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> - <td id="LC115" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">all</span> <span class="pl-k">=</span> <span class="pl-c1">all</span><span class="pl-k">+</span><span class="pl-c1">1</span></td> - </tr> - <tr> - <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> - <td id="LC116" class="blob-code blob-code-inner js-file-line"> ln <span class="pl-k">=</span> line[<span class="pl-c1">1</span>:] <span class="pl-c"><span class="pl-c">#</span>remove ></span></td> - </tr> - <tr> - <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> - <td id="LC117" class="blob-code blob-code-inner js-file-line"> ln <span class="pl-k">=</span> ln.rstrip() <span class="pl-c"><span class="pl-c">#</span>remove /n /r etc</span></td> - </tr> - <tr> - <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> - <td id="LC118" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (ln)</span></td> - </tr> - <tr> - <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> - <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> ln <span class="pl-k">in</span> gene_id_List:</td> - </tr> - <tr> - <td id="L120" class="blob-num js-line-number" data-line-number="120"></td> - <td id="LC120" class="blob-code blob-code-inner js-file-line"> number <span class="pl-k">=</span> number<span class="pl-k">+</span><span class="pl-c1">1</span></td> - </tr> - <tr> - <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> - <td id="LC121" class="blob-code blob-code-inner js-file-line"> outfile.write(line)</td> - </tr> - <tr> - <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> - <td id="LC122" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td> - </tr> - <tr> - <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> - <td id="LC123" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line:</td> - </tr> - <tr> - <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> - <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">while</span> line[<span class="pl-c1">0</span>] <span class="pl-k">!=</span> <span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> - <td id="LC125" class="blob-code blob-code-inner js-file-line"> outfile.write(line)</td> - </tr> - <tr> - <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> - <td id="LC126" class="blob-code blob-code-inner js-file-line"> line<span class="pl-k">=</span>ref.readline()</td> - </tr> - <tr> - <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> - <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-k">not</span> line:</td> - </tr> - <tr> - <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> - <td id="LC128" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span><span class="pl-bu">;</span></td> - </tr> - <tr> - <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> - <td id="LC129" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> - </tr> - <tr> - <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> - <td id="LC130" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td> - </tr> - <tr> - <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> - <td id="LC131" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> - </tr> - <tr> - <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> - <td id="LC132" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span>ref.readline()</td> - </tr> - <tr> - <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> - <td id="LC133" class="blob-code blob-code-inner js-file-line"> ref.close()</td> - </tr> - <tr> - <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> - <td id="LC134" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-c1">str</span>(<span class="pl-c1">len</span>(gene_id_List))<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>:<span class="pl-pds">"</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(number)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> from <span class="pl-pds">"</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(<span class="pl-c1">all</span>))</td> - </tr> - <tr> - <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> - <td id="LC135" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> cuff_df</td> - </tr> - <tr> - <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> - <td id="LC136" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> - <td id="LC137" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">HMMerMotifSearch</span>(<span class="pl-smi">name</span>, <span class="pl-smi">strain</span>, <span class="pl-smi">cuff_df</span>):</td> - </tr> - <tr> - <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> - <td id="LC138" class="blob-code blob-code-inner js-file-line"> motifs <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>1<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>2a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>2b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>3<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>4a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>4b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>4c<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>5<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>6<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>7<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>8a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>8b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>9a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>9b<span class="pl-pds">'</span></span>,</td> - </tr> - <tr> - <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> - <td id="LC139" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>9c<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>10a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>10b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>11a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>11b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>12<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>13a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>13b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>13c<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>13d<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>14<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>15a<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>15b<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>15c<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> - <td id="LC140" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> - </tr> - <tr> - <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> - <td id="LC141" class="blob-code blob-code-inner js-file-line"> phylopath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Motifs/Phylotype<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> - <td id="LC142" class="blob-code blob-code-inner js-file-line"> lineCounts <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L143" class="blob-num js-line-number" data-line-number="143"></td> - <td id="LC143" class="blob-code blob-code-inner js-file-line"> compoundList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L144" class="blob-num js-line-number" data-line-number="144"></td> - <td id="LC144" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> m <span class="pl-k">in</span> motifs:</td> - </tr> - <tr> - <td id="L145" class="blob-num js-line-number" data-line-number="145"></td> - <td id="LC145" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>hmmsearch <span class="pl-pds">"</span></span><span class="pl-k">+</span>phylopath <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.hmm <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>_6frame.fas > Phy<span class="pl-pds">"</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.out<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L146" class="blob-num js-line-number" data-line-number="146"></td> - <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> - </tr> - <tr> - <td id="L147" class="blob-num js-line-number" data-line-number="147"></td> - <td id="LC147" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L148" class="blob-num js-line-number" data-line-number="148"></td> - <td id="LC148" class="blob-code blob-code-inner js-file-line"> hmmResult <span class="pl-k">=</span> <span class="pl-c1">open</span>(<span class="pl-s"><span class="pl-pds">"</span>Phy<span class="pl-pds">"</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.out<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">'</span>r<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L149" class="blob-num js-line-number" data-line-number="149"></td> - <td id="LC149" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Tc148[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,8}</span><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L150" class="blob-num js-line-number" data-line-number="150"></td> - <td id="LC150" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L151" class="blob-num js-line-number" data-line-number="151"></td> - <td id="LC151" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Tc148[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,8}</span><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L152" class="blob-num js-line-number" data-line-number="152"></td> - <td id="LC152" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L153" class="blob-num js-line-number" data-line-number="153"></td> - <td id="LC153" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>TcIL3000_[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,4}</span>_[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,5}</span><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L154" class="blob-num js-line-number" data-line-number="154"></td> - <td id="LC154" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L155" class="blob-num js-line-number" data-line-number="155"></td> - <td id="LC155" class="blob-code blob-code-inner js-file-line"> outList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L156" class="blob-num js-line-number" data-line-number="156"></td> - <td id="LC156" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> line <span class="pl-k">in</span> hmmResult:</td> - </tr> - <tr> - <td id="L157" class="blob-num js-line-number" data-line-number="157"></td> - <td id="LC157" class="blob-code blob-code-inner js-file-line"> m <span class="pl-k">=</span> re.search(regex, line)</td> - </tr> - <tr> - <td id="L158" class="blob-num js-line-number" data-line-number="158"></td> - <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> m:</td> - </tr> - <tr> - <td id="L159" class="blob-num js-line-number" data-line-number="159"></td> - <td id="LC159" class="blob-code blob-code-inner js-file-line"> outList.append(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>m.group())</td> - </tr> - <tr> - <td id="L160" class="blob-num js-line-number" data-line-number="160"></td> - <td id="LC160" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">+=</span> <span class="pl-c1">1</span></td> - </tr> - <tr> - <td id="L161" class="blob-num js-line-number" data-line-number="161"></td> - <td id="LC161" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> re.search(<span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>inclusion<span class="pl-pds">"</span></span>, line):</td> - </tr> - <tr> - <td id="L162" class="blob-num js-line-number" data-line-number="162"></td> - <td id="LC162" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>inclusion threshold reached<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L163" class="blob-num js-line-number" data-line-number="163"></td> - <td id="LC163" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span></td> - </tr> - <tr> - <td id="L164" class="blob-num js-line-number" data-line-number="164"></td> - <td id="LC164" class="blob-code blob-code-inner js-file-line"> compoundList.append(outList)</td> - </tr> - <tr> - <td id="L165" class="blob-num js-line-number" data-line-number="165"></td> - <td id="LC165" class="blob-code blob-code-inner js-file-line"> lineCounts.append(n)</td> - </tr> - <tr> - <td id="L166" class="blob-num js-line-number" data-line-number="166"></td> - <td id="LC166" class="blob-code blob-code-inner js-file-line"> hmmResult.close()</td> - </tr> - <tr> - <td id="L167" class="blob-num js-line-number" data-line-number="167"></td> - <td id="LC167" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(lineCounts)</span></td> - </tr> - <tr> - <td id="L168" class="blob-num js-line-number" data-line-number="168"></td> - <td id="LC168" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L169" class="blob-num js-line-number" data-line-number="169"></td> - <td id="LC169" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(cuff_df)</span></td> - </tr> - <tr> - <td id="L170" class="blob-num js-line-number" data-line-number="170"></td> - <td id="LC170" class="blob-code blob-code-inner js-file-line"> concatGroups <span class="pl-k">=</span> [<span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">3</span>, <span class="pl-c1">2</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">4</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>]</td> - </tr> - <tr> - <td id="L171" class="blob-num js-line-number" data-line-number="171"></td> - <td id="LC171" class="blob-code blob-code-inner js-file-line"> countList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L172" class="blob-num js-line-number" data-line-number="172"></td> - <td id="LC172" class="blob-code blob-code-inner js-file-line"> weightList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L173" class="blob-num js-line-number" data-line-number="173"></td> - <td id="LC173" class="blob-code blob-code-inner js-file-line"> countIndex <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L174" class="blob-num js-line-number" data-line-number="174"></td> - <td id="LC174" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L175" class="blob-num js-line-number" data-line-number="175"></td> - <td id="LC175" class="blob-code blob-code-inner js-file-line"> totalWeigth <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L176" class="blob-num js-line-number" data-line-number="176"></td> - <td id="LC176" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> c <span class="pl-k">in</span> concatGroups:</td> - </tr> - <tr> - <td id="L177" class="blob-num js-line-number" data-line-number="177"></td> - <td id="LC177" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L178" class="blob-num js-line-number" data-line-number="178"></td> - <td id="LC178" class="blob-code blob-code-inner js-file-line"> weight <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L179" class="blob-num js-line-number" data-line-number="179"></td> - <td id="LC179" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, c):</td> - </tr> - <tr> - <td id="L180" class="blob-num js-line-number" data-line-number="180"></td> - <td id="LC180" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> a <span class="pl-k">+</span> compoundList.pop(<span class="pl-c1">0</span>)</td> - </tr> - <tr> - <td id="L181" class="blob-num js-line-number" data-line-number="181"></td> - <td id="LC181" class="blob-code blob-code-inner js-file-line"> t <span class="pl-k">=</span> <span class="pl-c1">set</span>(a)</td> - </tr> - <tr> - <td id="L182" class="blob-num js-line-number" data-line-number="182"></td> - <td id="LC182" class="blob-code blob-code-inner js-file-line"> countList.append(<span class="pl-c1">len</span>(t))</td> - </tr> - <tr> - <td id="L183" class="blob-num js-line-number" data-line-number="183"></td> - <td id="LC183" class="blob-code blob-code-inner js-file-line"> wa <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L184" class="blob-num js-line-number" data-line-number="184"></td> - <td id="LC184" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> w <span class="pl-k">in</span> t:</td> - </tr> - <tr> - <td id="L185" class="blob-num js-line-number" data-line-number="185"></td> - <td id="LC185" class="blob-code blob-code-inner js-file-line"> wt <span class="pl-k">=</span> cuff_df.loc[cuff_df[<span class="pl-s"><span class="pl-pds">'</span>gene_id<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> w, <span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].iloc[<span class="pl-c1">0</span>]</td> - </tr> - <tr> - <td id="L186" class="blob-num js-line-number" data-line-number="186"></td> - <td id="LC186" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(w)</span></td> - </tr> - <tr> - <td id="L187" class="blob-num js-line-number" data-line-number="187"></td> - <td id="LC187" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(wt)</span></td> - </tr> - <tr> - <td id="L188" class="blob-num js-line-number" data-line-number="188"></td> - <td id="LC188" class="blob-code blob-code-inner js-file-line"> wa <span class="pl-k">=</span> wa<span class="pl-k">+</span>wt</td> - </tr> - <tr> - <td id="L189" class="blob-num js-line-number" data-line-number="189"></td> - <td id="LC189" class="blob-code blob-code-inner js-file-line"> weightList.append(wa)</td> - </tr> - <tr> - <td id="L190" class="blob-num js-line-number" data-line-number="190"></td> - <td id="LC190" class="blob-code blob-code-inner js-file-line"> totalWeigth<span class="pl-k">+=</span>wa</td> - </tr> - <tr> - <td id="L191" class="blob-num js-line-number" data-line-number="191"></td> - <td id="LC191" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">+=</span> <span class="pl-c1">len</span>(t)</td> - </tr> - <tr> - <td id="L192" class="blob-num js-line-number" data-line-number="192"></td> - <td id="LC192" class="blob-code blob-code-inner js-file-line"> countList.append(totalCount)</td> - </tr> - <tr> - <td id="L193" class="blob-num js-line-number" data-line-number="193"></td> - <td id="LC193" class="blob-code blob-code-inner js-file-line"> weightList.append(totalWeigth)</td> - </tr> - <tr> - <td id="L194" class="blob-num js-line-number" data-line-number="194"></td> - <td id="LC194" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(countList)</span></td> - </tr> - <tr> - <td id="L195" class="blob-num js-line-number" data-line-number="195"></td> - <td id="LC195" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("--------")</span></td> - </tr> - <tr> - <td id="L196" class="blob-num js-line-number" data-line-number="196"></td> - <td id="LC196" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(weightList)</span></td> - </tr> - <tr> - <td id="L197" class="blob-num js-line-number" data-line-number="197"></td> - <td id="LC197" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("--------")</span></td> - </tr> - <tr> - <td id="L198" class="blob-num js-line-number" data-line-number="198"></td> - <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> countList,weightList</td> - </tr> - <tr> - <td id="L199" class="blob-num js-line-number" data-line-number="199"></td> - <td id="LC199" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L200" class="blob-num js-line-number" data-line-number="200"></td> - <td id="LC200" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">relativeFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td> - </tr> - <tr> - <td id="L201" class="blob-num js-line-number" data-line-number="201"></td> - <td id="LC201" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L202" class="blob-num js-line-number" data-line-number="202"></td> - <td id="LC202" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</span>])</td> - </tr> - <tr> - <td id="L203" class="blob-num js-line-number" data-line-number="203"></td> - <td id="LC203" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td> - </tr> - <tr> - <td id="L204" class="blob-num js-line-number" data-line-number="204"></td> - <td id="LC204" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td> - </tr> - <tr> - <td id="L205" class="blob-num js-line-number" data-line-number="205"></td> - <td id="LC205" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L206" class="blob-num js-line-number" data-line-number="206"></td> - <td id="LC206" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>: pList, <span class="pl-s"><span class="pl-pds">'</span>Relative Frequency<span class="pl-pds">'</span></span>: relFreqList}</td> - </tr> - <tr> - <td id="L207" class="blob-num js-line-number" data-line-number="207"></td> - <td id="LC207" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td> - </tr> - <tr> - <td id="L208" class="blob-num js-line-number" data-line-number="208"></td> - <td id="LC208" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> htmlresource<span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</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>_t_relative_frequency.csv<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L209" class="blob-num js-line-number" data-line-number="209"></td> - <td id="LC209" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td> - </tr> - <tr> - <td id="L210" class="blob-num js-line-number" data-line-number="210"></td> - <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> relFreqList <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></td> - </tr> - <tr> - <td id="L211" class="blob-num js-line-number" data-line-number="211"></td> - <td id="LC211" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L212" class="blob-num js-line-number" data-line-number="212"></td> - <td id="LC212" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L213" class="blob-num js-line-number" data-line-number="213"></td> - <td id="LC213" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">weightedFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td> - </tr> - <tr> - <td id="L214" class="blob-num js-line-number" data-line-number="214"></td> - <td id="LC214" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L215" class="blob-num js-line-number" data-line-number="215"></td> - <td id="LC215" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</span>])</td> - </tr> - <tr> - <td id="L216" class="blob-num js-line-number" data-line-number="216"></td> - <td id="LC216" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td> - </tr> - <tr> - <td id="L217" class="blob-num js-line-number" data-line-number="217"></td> - <td id="LC217" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td> - </tr> - <tr> - <td id="L218" class="blob-num js-line-number" data-line-number="218"></td> - <td id="LC218" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L219" class="blob-num js-line-number" data-line-number="219"></td> - <td id="LC219" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>: pList, <span class="pl-s"><span class="pl-pds">'</span>Weighted Frequency<span class="pl-pds">'</span></span>: relFreqList}</td> - </tr> - <tr> - <td id="L220" class="blob-num js-line-number" data-line-number="220"></td> - <td id="LC220" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td> - </tr> - <tr> - <td id="L221" class="blob-num js-line-number" data-line-number="221"></td> - <td id="LC221" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> htmlresource<span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</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>_t_weighted_frequency.csv<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L222" class="blob-num js-line-number" data-line-number="222"></td> - <td id="LC222" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td> - </tr> - <tr> - <td id="L223" class="blob-num js-line-number" data-line-number="223"></td> - <td id="LC223" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> relFreqList <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></td> - </tr> - <tr> - <td id="L224" class="blob-num js-line-number" data-line-number="224"></td> - <td id="LC224" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L225" class="blob-num js-line-number" data-line-number="225"></td> - <td id="LC225" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L226" class="blob-num js-line-number" data-line-number="226"></td> - <td id="LC226" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L227" class="blob-num js-line-number" data-line-number="227"></td> - <td id="LC227" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createStackedBar</span>(<span class="pl-smi">name</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">strain</span>,<span class="pl-smi">pdf</span>,<span class="pl-smi">html_resource</span>):</td> - </tr> - <tr> - <td id="L228" class="blob-num js-line-number" data-line-number="228"></td> - <td id="LC228" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">"</span>#0000ff<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#6495ed<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#00ffff<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#caff70<span class="pl-pds">"</span></span>,</td> - </tr> - <tr> - <td id="L229" class="blob-num js-line-number" data-line-number="229"></td> - <td id="LC229" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>#228b22<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#528b8b<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#00ff00<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#a52a2a<span class="pl-pds">"</span></span>,</td> - </tr> - <tr> - <td id="L230" class="blob-num js-line-number" data-line-number="230"></td> - <td id="LC230" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>#ff0000<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#ffff00<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#ffa500<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#ff1493<span class="pl-pds">"</span></span>,</td> - </tr> - <tr> - <td id="L231" class="blob-num js-line-number" data-line-number="231"></td> - <td id="LC231" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>#9400d3<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#bebebe<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#000000<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>#ff00ff<span class="pl-pds">"</span></span>]</td> - </tr> - <tr> - <td id="L232" class="blob-num js-line-number" data-line-number="232"></td> - <td id="LC232" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L233" class="blob-num js-line-number" data-line-number="233"></td> - <td id="LC233" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">VAP_148</span> <span class="pl-k">=</span> [<span class="pl-c1">0.072</span>, <span class="pl-c1">0.032</span>, <span class="pl-c1">0.032</span>, <span class="pl-c1">0.004</span>, <span class="pl-c1">0.007</span>,</td> - </tr> - <tr> - <td id="L234" class="blob-num js-line-number" data-line-number="234"></td> - <td id="LC234" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.005</span>, <span class="pl-c1">0.202</span>, <span class="pl-c1">0.004</span>, <span class="pl-c1">0.006</span>, <span class="pl-c1">0.014</span>,</td> - </tr> - <tr> - <td id="L235" class="blob-num js-line-number" data-line-number="235"></td> - <td id="LC235" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.130</span>, <span class="pl-c1">0.133</span>, <span class="pl-c1">0.054</span>, <span class="pl-c1">0.039</span>, <span class="pl-c1">0.265</span>]</td> - </tr> - <tr> - <td id="L236" class="blob-num js-line-number" data-line-number="236"></td> - <td id="LC236" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L237" class="blob-num js-line-number" data-line-number="237"></td> - <td id="LC237" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">VAP_IL3000</span> <span class="pl-k">=</span> [<span class="pl-c1">0.073</span>, <span class="pl-c1">0.040</span>, <span class="pl-c1">0.049</span>, <span class="pl-c1">0.018</span>, <span class="pl-c1">0.060</span>,</td> - </tr> - <tr> - <td id="L238" class="blob-num js-line-number" data-line-number="238"></td> - <td id="LC238" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.055</span>, <span class="pl-c1">0.054</span>, <span class="pl-c1">0.025</span>, <span class="pl-c1">0.012</span>, <span class="pl-c1">0.060</span>,</td> - </tr> - <tr> - <td id="L239" class="blob-num js-line-number" data-line-number="239"></td> - <td id="LC239" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.142</span>, <span class="pl-c1">0.100</span>, <span class="pl-c1">0.061</span>, <span class="pl-c1">0.078</span>, <span class="pl-c1">0.172</span>]</td> - </tr> - <tr> - <td id="L240" class="blob-num js-line-number" data-line-number="240"></td> - <td id="LC240" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab20<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"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td> - </tr> - <tr> - <td id="L242" class="blob-num js-line-number" data-line-number="242"></td> - <td id="LC242" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L243" class="blob-num js-line-number" data-line-number="243"></td> - <td id="LC243" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>Tc148<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"> VAPtable <span class="pl-k">=</span> <span class="pl-c1">VAP_148</span></td> - </tr> - <tr> - <td id="L245" class="blob-num js-line-number" data-line-number="245"></td> - <td id="LC245" class="blob-code blob-code-inner js-file-line"> VAPname<span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>Tc148<span class="pl-cce">\n</span>Genome VAP<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"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>IL3000<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"> VAPtable <span class="pl-k">=</span> <span class="pl-c1">VAP_IL3000</span></td> - </tr> - <tr> - <td id="L248" class="blob-num js-line-number" data-line-number="248"></td> - <td id="LC248" class="blob-code blob-code-inner js-file-line"> VAPname<span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>IL3000<span class="pl-cce">\n</span>Genome VAP<span class="pl-pds">'</span></span></td> - </tr> - <tr> - <td id="L249" class="blob-num js-line-number" data-line-number="249"></td> - <td id="LC249" class="blob-code blob-code-inner js-file-line"> width <span class="pl-k">=</span> <span class="pl-c1">0.35</span> <span class="pl-c"><span class="pl-c">#</span> the width of the bars: can also be len(x) sequence</span></td> - </tr> - <tr> - <td id="L250" class="blob-num js-line-number" data-line-number="250"></td> - <td id="LC250" class="blob-code blob-code-inner js-file-line"> plots <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L251" class="blob-num js-line-number" data-line-number="251"></td> - <td id="LC251" class="blob-code blob-code-inner js-file-line"> fpos <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L252" class="blob-num js-line-number" data-line-number="252"></td> - <td id="LC252" class="blob-code blob-code-inner js-file-line"> vpos <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L253" class="blob-num js-line-number" data-line-number="253"></td> - <td id="LC253" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td> - </tr> - <tr> - <td id="L254" class="blob-num js-line-number" data-line-number="254"></td> - <td id="LC254" class="blob-code blob-code-inner js-file-line"> tp <span class="pl-k">=</span> plt.bar(<span class="pl-c1">0</span>, freqList[p], width, <span class="pl-v">color</span><span class="pl-k">=</span> palette[p], <span class="pl-v">bottom</span> <span class="pl-k">=</span> fpos)</td> - </tr> - <tr> - <td id="L255" class="blob-num js-line-number" data-line-number="255"></td> - <td id="LC255" class="blob-code blob-code-inner js-file-line"> fpos <span class="pl-k">+=</span>freqList[p]</td> - </tr> - <tr> - <td id="L256" class="blob-num js-line-number" data-line-number="256"></td> - <td id="LC256" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L257" class="blob-num js-line-number" data-line-number="257"></td> - <td id="LC257" class="blob-code blob-code-inner js-file-line"> tp <span class="pl-k">=</span> plt.bar(<span class="pl-c1">1</span>, VAPtable[p], width, <span class="pl-v">color</span><span class="pl-k">=</span> palette[p], <span class="pl-v">bottom</span> <span class="pl-k">=</span> vpos)</td> - </tr> - <tr> - <td id="L258" class="blob-num js-line-number" data-line-number="258"></td> - <td id="LC258" class="blob-code blob-code-inner js-file-line"> vpos <span class="pl-k">+=</span>VAPtable[p]</td> - </tr> - <tr> - <td id="L259" class="blob-num js-line-number" data-line-number="259"></td> - <td id="LC259" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L260" class="blob-num js-line-number" data-line-number="260"></td> - <td id="LC260" class="blob-code blob-code-inner js-file-line"> plots.append(tp)</td> - </tr> - <tr> - <td id="L261" class="blob-num js-line-number" data-line-number="261"></td> - <td id="LC261" class="blob-code blob-code-inner js-file-line"> plt.xticks([<span class="pl-c1">0</span>,<span class="pl-c1">1</span>],[name,VAPname])</td> - </tr> - <tr> - <td id="L262" class="blob-num js-line-number" data-line-number="262"></td> - <td id="LC262" class="blob-code blob-code-inner js-file-line"> plt.legend(plots[::<span class="pl-k">-</span><span class="pl-c1">1</span>],[<span class="pl-s"><span class="pl-pds">'</span>p15<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p14<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p13<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p12<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p11<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p10<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p9<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p8<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p7<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p6<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p5<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p4<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p3<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p2<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>p1<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L263" class="blob-num js-line-number" data-line-number="263"></td> - <td id="LC263" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Figure Legend: The transcriptomic Variant Antigen Profile of $\itTrypanosoma$ $\itcongolense$ estimated as phylotype <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L264" class="blob-num js-line-number" data-line-number="264"></td> - <td id="LC264" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>proportion adjusted for transcript abundance and the reference genomic Variant Antigen Profile. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L265" class="blob-num js-line-number" data-line-number="265"></td> - <td id="LC265" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>Data was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L266" class="blob-num js-line-number" data-line-number="266"></td> - <td id="LC266" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.title(title, wrap="True")</span></td> - </tr> - <tr> - <td id="L267" class="blob-num js-line-number" data-line-number="267"></td> - <td id="LC267" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.text(-0.2, -0.05, title, va="top", transform=ax.transAxes, wrap="True")</span></td> - </tr> - <tr> - <td id="L268" class="blob-num js-line-number" data-line-number="268"></td> - <td id="LC268" class="blob-code blob-code-inner js-file-line"> plt.text(<span class="pl-k">-</span><span class="pl-c1">0.3</span>, <span class="pl-k">-</span><span class="pl-c1">0.15</span>, title, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</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="L269" class="blob-num js-line-number" data-line-number="269"></td> - <td id="LC269" class="blob-code blob-code-inner js-file-line"> plt.tight_layout(<span class="pl-v">pad</span><span class="pl-k">=</span><span class="pl-c1">1.5</span>)</td> - </tr> - <tr> - <td id="L270" class="blob-num js-line-number" data-line-number="270"></td> - <td id="LC270" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span> <span class="pl-k">=</span> <span class="pl-c1">0.3</span>,<span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.99</span>,<span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.125</span>,<span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>,<span class="pl-v">hspace</span><span class="pl-k">=</span><span class="pl-c1">0.2</span>,<span class="pl-v">wspace</span><span class="pl-k">=</span><span class="pl-c1">0.2</span>)</td> - </tr> - <tr> - <td id="L271" class="blob-num js-line-number" data-line-number="271"></td> - <td id="LC271" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L272" class="blob-num js-line-number" data-line-number="272"></td> - <td id="LC272" class="blob-code blob-code-inner js-file-line"> plt.savefig(html_resource <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/stackedbar.png<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"> <span class="pl-k">if</span> pdf <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="L274" class="blob-num js-line-number" data-line-number="274"></td> - <td id="LC274" class="blob-code blob-code-inner js-file-line"> plt.savefig(html_resource <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/stackedbar.pdf<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"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td> - </tr> - <tr> - <td id="L276" class="blob-num js-line-number" data-line-number="276"></td> - <td id="LC276" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L277" class="blob-num js-line-number" data-line-number="277"></td> - <td id="LC277" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L278" class="blob-num js-line-number" data-line-number="278"></td> - <td id="LC278" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">name</span>,<span class="pl-smi">htmlfn</span>,<span class="pl-smi">htmlresource</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">weightList</span>):</td> - </tr> - <tr> - <td id="L279" class="blob-num js-line-number" data-line-number="279"></td> - <td id="LC279" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td> - </tr> - <tr> - <td id="L280" class="blob-num js-line-number" data-line-number="280"></td> - <td id="LC280" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>congolense VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma congolense</i> Variant Antigen Profile</h2><h3><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"> htmlString <span class="pl-k">+=</span> name</td> - </tr> - <tr> - <td id="L282" class="blob-num js-line-number" data-line-number="282"></td> - <td id="LC282" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L283" class="blob-num js-line-number" data-line-number="283"></td> - <td id="LC283" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Table Legend: Variant Antigen Profiles of a transcriptome of <i>Trypanosoma congolense</i> estimated as phylotype proportion. <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"> <span class="pl-s"><span class="pl-pds">"</span>Weighted frequency refers to the phylotype proportion based transcript abundance. <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"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L286" class="blob-num js-line-number" data-line-number="286"></td> - <td id="LC286" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L287" class="blob-num js-line-number" data-line-number="287"></td> - <td id="LC287" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L288" class="blob-num js-line-number" data-line-number="288"></td> - <td id="LC288" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><th>Relative Frequency</th><th>Weighted Frequency</th></tr><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L289" class="blob-num js-line-number" data-line-number="289"></td> - <td id="LC289" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L290" class="blob-num js-line-number" data-line-number="290"></td> - <td id="LC290" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></td> - </tr> - <tr> - <td id="L291" class="blob-num js-line-number" data-line-number="291"></td> - <td id="LC291" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td> - </tr> - <tr> - <td id="L292" class="blob-num js-line-number" data-line-number="292"></td> - <td id="LC292" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(freqList[i], <span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L293" class="blob-num js-line-number" data-line-number="293"></td> - <td id="LC293" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">format</span>(weightList[i], <span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L294" class="blob-num js-line-number" data-line-number="294"></td> - <td id="LC294" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td>phy<span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(i <span class="pl-k">+</span> <span class="pl-c1">1</span>) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> f <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> w <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td></tr><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L295" class="blob-num js-line-number" data-line-number="295"></td> - <td id="LC295" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L296" class="blob-num js-line-number" data-line-number="296"></td> - <td id="LC296" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><p> <h3>Stacked Bar chart of Phylotype Frequency</h3> The 'weighted' relative frequency of each phylotype alongside the VAP of selected strain<span class="pl-c1">.</span></p><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L297" class="blob-num js-line-number" data-line-number="297"></td> - <td id="LC297" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = 'stackedbar<span class="pl-c1">.</span>png' alt='Stacked bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L298" class="blob-num js-line-number" data-line-number="298"></td> - <td id="LC298" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> - </tr> - <tr> - <td id="L299" class="blob-num js-line-number" data-line-number="299"></td> - <td id="LC299" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L300" class="blob-num js-line-number" data-line-number="300"></td> - <td id="LC300" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += r"<p><h3>The Deviation Heat Map and Dendogram</h3>The phylotype variation expressed as the deviation from your sample mean compared to the model dataset</p>"</span></td> - </tr> - <tr> - <td id="L301" class="blob-num js-line-number" data-line-number="301"></td> - <td id="LC301" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> imgString = r"<img src = 'dheatmap.png' alt='Deviation Heatmap' style='max-width:100%'><br><br>"</span></td> - </tr> - <tr> - <td id="L302" class="blob-num js-line-number" data-line-number="302"></td> - <td id="LC302" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += imgString</span></td> - </tr> - <tr> - <td id="L303" class="blob-num js-line-number" data-line-number="303"></td> - <td id="LC303" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L304" class="blob-num js-line-number" data-line-number="304"></td> - <td id="LC304" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += r"<p><h3>The Variation PCA plot</h3>PCA analysis corresponding to absolute variation. Colour coded according to location</p>"</span></td> - </tr> - <tr> - <td id="L305" class="blob-num js-line-number" data-line-number="305"></td> - <td id="LC305" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> imgString = r"<img src = 'vapPCA.png' alt='PCA Analysis' style='max-width:100%'><br><br>"</span></td> - </tr> - <tr> - <td id="L306" class="blob-num js-line-number" data-line-number="306"></td> - <td id="LC306" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += imgString + r"</div></body></html>"</span></td> - </tr> - <tr> - <td id="L307" class="blob-num js-line-number" data-line-number="307"></td> - <td id="LC307" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L308" class="blob-num js-line-number" data-line-number="308"></td> - <td id="LC308" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(htmlfn, <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td> - </tr> - <tr> - <td id="L309" class="blob-num js-line-number" data-line-number="309"></td> - <td id="LC309" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> - </tr> - <tr> - <td id="L310" class="blob-num js-line-number" data-line-number="310"></td> - <td id="LC310" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L311" class="blob-num js-line-number" data-line-number="311"></td> - <td id="LC311" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}</span></td> - </tr> - <tr> - <td id="L312" class="blob-num js-line-number" data-line-number="312"></td> - <td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptomicProcess</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td> - </tr> - <tr> - <td id="L313" class="blob-num js-line-number" data-line-number="313"></td> - <td id="LC313" class="blob-code blob-code-inner js-file-line"> transcriptMapping(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]], 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>]]) <span class="pl-c"><span class="pl-c">#</span>uses bowtie</span></td> - </tr> - <tr> - <td id="L314" class="blob-num js-line-number" data-line-number="314"></td> - <td id="LC314" class="blob-code blob-code-inner js-file-line"> processSamFiles(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span>uses samtools</span></td> - </tr> - <tr> - <td id="L315" class="blob-num js-line-number" data-line-number="315"></td> - <td id="LC315" class="blob-code blob-code-inner js-file-line"> transcriptAbundance(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]]) <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -> ?.cuff/*.*</span></td> - </tr> - <tr> - <td id="L316" class="blob-num js-line-number" data-line-number="316"></td> - <td id="LC316" class="blob-code blob-code-inner js-file-line"> cuff_df <span class="pl-k">=</span> convertToFasta(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]])</td> - </tr> - <tr> - <td id="L317" class="blob-num js-line-number" data-line-number="317"></td> - <td id="LC317" class="blob-code blob-code-inner js-file-line"> countList, weightList <span class="pl-k">=</span> HMMerMotifSearch(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]], cuff_df)</td> - </tr> - <tr> - <td id="L318" class="blob-num js-line-number" data-line-number="318"></td> - <td id="LC318" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> relativeFrequencyTable(countList,args[dict[<span class="pl-s"><span class="pl-pds">'</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>]])</td> - </tr> - <tr> - <td id="L319" class="blob-num js-line-number" data-line-number="319"></td> - <td id="LC319" class="blob-code blob-code-inner js-file-line"> relWeightList <span class="pl-k">=</span> weightedFrequencyTable(weightList,args[dict[<span class="pl-s"><span class="pl-pds">'</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>]])</td> - </tr> - <tr> - <td id="L320" class="blob-num js-line-number" data-line-number="320"></td> - <td id="LC320" class="blob-code blob-code-inner js-file-line"> createStackedBar(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]],relWeightList, args[dict[<span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<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="L321" class="blob-num js-line-number" data-line-number="321"></td> - <td id="LC321" class="blob-code blob-code-inner js-file-line"> createHTML(args[dict[<span class="pl-s"><span class="pl-pds">'</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>]], relFreqList, relWeightList)</td> - </tr> - <tr> - <td id="L322" class="blob-num js-line-number" data-line-number="322"></td> - <td id="LC322" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L323" class="blob-num js-line-number" data-line-number="323"></td> - <td id="LC323" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>__main__<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L324" class="blob-num js-line-number" data-line-number="324"></td> - <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("Commencing Transcript Mapping")</span></td> - </tr> - <tr> - <td id="L325" class="blob-num js-line-number" data-line-number="325"></td> - <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>transcriptMapping("T_Test", "Transcripts.1","Transcripts.2")</span></td> - </tr> - <tr> - <td id="L326" class="blob-num js-line-number" data-line-number="326"></td> - <td id="LC326" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("Processimg Sam Files")</span></td> - </tr> - <tr> - <td id="L327" class="blob-num js-line-number" data-line-number="327"></td> - <td id="LC327" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>processSamFiles("T_Test")</span></td> - </tr> - <tr> - <td id="L328" class="blob-num js-line-number" data-line-number="328"></td> - <td id="LC328" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("Assessing Transcript Abundance")</span></td> - </tr> - <tr> - <td id="L329" class="blob-num js-line-number" data-line-number="329"></td> - <td id="LC329" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>transcriptAbundance("T_Test")</span></td> - </tr> - <tr> - <td id="L330" class="blob-num js-line-number" data-line-number="330"></td> - <td id="LC330" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print ("Converting to Fasta Subset")</span></td> - </tr> - <tr> - <td id="L331" class="blob-num js-line-number" data-line-number="331"></td> - <td id="LC331" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cuff_df = convertToFasta("T_Test")</span></td> - </tr> - <tr> - <td id="L332" class="blob-num js-line-number" data-line-number="332"></td> - <td id="LC332" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("Commencing HMMer search")</span></td> - </tr> - <tr> - <td id="L333" class="blob-num js-line-number" data-line-number="333"></td> - <td id="LC333" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>countList, weightList = HMMerMotifSearch("T_Test",cuff_df)</span></td> - </tr> - <tr> - <td id="L334" class="blob-num js-line-number" data-line-number="334"></td> - <td id="LC334" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>relativeFrequencyTable(countList,'T_Test')</span></td> - </tr> - <tr> - <td id="L335" class="blob-num js-line-number" data-line-number="335"></td> - <td id="LC335" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>weightedFrequencyTable(weightList,'T_Test')</span></td> - </tr> - <tr> - <td id="L336" class="blob-num js-line-number" data-line-number="336"></td> - <td id="LC336" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> [<span class="pl-c1">0.111842105</span>,<span class="pl-c1">0.059210526</span>,<span class="pl-c1">0.026315789</span>,<span class="pl-c1">0.013157895</span>,</td> - </tr> - <tr> - <td id="L337" class="blob-num js-line-number" data-line-number="337"></td> - <td id="LC337" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.006578947</span>,<span class="pl-c1">0.013157895</span>,<span class="pl-c1">0.032894737</span>,<span class="pl-c1">0.019736842</span>,</td> - </tr> - <tr> - <td id="L338" class="blob-num js-line-number" data-line-number="338"></td> - <td id="LC338" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.039473684</span>,<span class="pl-c1">0.046052632</span>,<span class="pl-c1">0.217105263</span>,<span class="pl-c1">0.065789474</span>,</td> - </tr> - <tr> - <td id="L339" class="blob-num js-line-number" data-line-number="339"></td> - <td id="LC339" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.151315789</span>,<span class="pl-c1">0.059210526</span>,<span class="pl-c1">0.138157895</span>]</td> - </tr> - <tr> - <td id="L340" class="blob-num js-line-number" data-line-number="340"></td> - <td id="LC340" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L341" class="blob-num js-line-number" data-line-number="341"></td> - <td id="LC341" class="blob-code blob-code-inner js-file-line"> relWeightList <span class="pl-k">=</span> [<span class="pl-c1">0.07532571</span>,<span class="pl-c1">0.05900545</span>,<span class="pl-c1">0.009601452</span>,<span class="pl-c1">0.042357532</span>,<span class="pl-c1">0.01236219</span>,<span class="pl-c1">0.001675663</span>,<span class="pl-c1">0.04109726</span>,</td> - </tr> - <tr> - <td id="L342" class="blob-num js-line-number" data-line-number="342"></td> - <td id="LC342" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.097464248</span>,<span class="pl-c1">0.057491666</span>,<span class="pl-c1">0.05826875</span>,<span class="pl-c1">0.279457473</span>,<span class="pl-c1">0.070004772</span>,<span class="pl-c1">0.065329007</span>,<span class="pl-c1">0.085361298</span>,<span class="pl-c1">0.045197529</span>]</td> - </tr> - <tr> - <td id="L343" class="blob-num js-line-number" data-line-number="343"></td> - <td id="LC343" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L344" class="blob-num js-line-number" data-line-number="344"></td> - <td id="LC344" class="blob-code blob-code-inner js-file-line"> createStackedBar(<span class="pl-s"><span class="pl-pds">'</span>T_Test<span class="pl-pds">'</span></span>,relWeightList, <span class="pl-s"><span class="pl-pds">'</span>Tc148<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>results<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L345" class="blob-num js-line-number" data-line-number="345"></td> - <td id="LC345" class="blob-code blob-code-inner js-file-line"> createHTML(<span class="pl-s"><span class="pl-pds">"</span>t_test<span class="pl-pds">"</span></span>,<span class="pl-s"><span class="pl-pds">"</span>results/t_test.html<span class="pl-pds">"</span></span>,<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>,relFreqList,relWeightList)</td> - </tr> -</table> +def HMMerMotifSearch(name, strain, cuff_df): + motifs = ['1', '2a', '2b', '3', '4a', '4b', '4c', '5', '6', '7', '8a', '8b', '9a', '9b', + '9c', '10a', '10b', '11a', '11b', '12', '13a', '13b', '13c', '13d', '14', '15a', '15b', '15c'] + dir_path = os.path.dirname(os.path.realpath(__file__)) + phylopath = dir_path + "/data/Motifs/Phylotype" + lineCounts = [] + compoundList = [] + for m in motifs: + argString = "hmmsearch "+phylopath + m + ".hmm " + name + "_6frame.fas > Phy" + m + ".out" + print(argString) + subprocess.call(argString, shell=True) + hmmResult = open("Phy" + m + ".out", 'r') + regex = r"Tc148[0-9]{1,8}" + if strain == "Tc148": + regex = r"Tc148[0-9]{1,8}" + if strain == "IL3000": + regex = r"TcIL3000_[0-9]{1,4}_[0-9]{1,5}" + n = 0 + outList = [] + for line in hmmResult: + m = re.search(regex, line) + if m: + outList.append(""+m.group()) + n += 1 + if re.search(r"inclusion", line): + print("inclusion threshold reached") + break + compoundList.append(outList) + lineCounts.append(n) + hmmResult.close() + #print(lineCounts) - <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true"> - <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar"> - <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg> - </summary> - <details-menu> - <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px"> - <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li> - <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li> - <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/johnheap/VAPPER-Galaxy/blame/a4e16d71fe985f389930c02f94354b87d3aabadb/Tryp_T.py">View git blame</a></li> - <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li> - </ul> - </details-menu> - </details> + #print(cuff_df) + concatGroups = [1, 2, 1, 3, 1, 1, 1, 2, 3, 2, 2, 1, 4, 1, 3] + countList = [] + weightList = [] + countIndex = 0 + totalCount = 0 + totalWeigth = 0 + for c in concatGroups: + a = [] + weight = [] + for n in range(0, c): + a = a + compoundList.pop(0) + t = set(a) + countList.append(len(t)) + wa = 0 + for w in t: + wt = cuff_df.loc[cuff_df['gene_id'] == w, 'FPKM'].iloc[0] + #print(w) + #print(wt) + wa = wa+wt + weightList.append(wa) + totalWeigth+=wa + totalCount += len(t) + countList.append(totalCount) + weightList.append(totalWeigth) + #print(countList) + #print("--------") + #print(weightList) + #print("--------") + return countList,weightList - </div> +def relativeFrequencyTable(countList, name, htmlresource): + relFreqList = [] + c = float(countList[15]) + for i in range(0, 15): + relFreqList.append(countList[i] / c) - </div> - - + data = {'Phylotype': pList, 'Relative Frequency': relFreqList} + relFreq_df = pd.DataFrame(data) + j_fname = htmlresource+ "/" + name + "_t_relative_frequency.csv" + relFreq_df.to_csv(j_fname) + return relFreqList # 0-14 = p1-p15 counts [15] = total counts - <details class="details-reset details-overlay details-overlay-dark"> - <summary data-hotkey="l" aria-label="Jump to line"></summary> - <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line"> - <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> - <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus> - <button type="submit" class="btn" data-close-dialog>Go</button> -</form> </details-dialog> - </details> + +def weightedFrequencyTable(countList, name, htmlresource): + relFreqList = [] + c = float(countList[15]) + for i in range(0, 15): + relFreqList.append(countList[i] / c) + + data = {'Phylotype': pList, 'Weighted Frequency': relFreqList} + relFreq_df = pd.DataFrame(data) + j_fname = htmlresource+ "/" + name + "_t_weighted_frequency.csv" + relFreq_df.to_csv(j_fname) + return relFreqList # 0-14 = p1-p15 counts [15] = total counts - </div> - <div class="modal-backdrop js-touch-events"></div> -</div> +def createStackedBar(name,freqList,strain,pdf,html_resource): + palette = ["#0000ff", "#6495ed", "#00ffff", "#caff70", + "#228b22", "#528b8b", "#00ff00", "#a52a2a", + "#ff0000", "#ffff00", "#ffa500", "#ff1493", + "#9400d3", "#bebebe", "#000000", "#ff00ff"] - </main> - </div> - + VAP_148 = [0.072, 0.032, 0.032, 0.004, 0.007, + 0.005, 0.202, 0.004, 0.006, 0.014, + 0.130, 0.133, 0.054, 0.039, 0.265] - </div> + VAP_IL3000 = [0.073, 0.040, 0.049, 0.018, 0.060, + 0.055, 0.054, 0.025, 0.012, 0.060, + 0.142, 0.100, 0.061, 0.078, 0.172] + cmap = plt.cm.get_cmap('tab20') + palette = [cmap(i) for i in range(cmap.N)] - -<div class="footer container-lg width-full p-responsive" role="contentinfo"> - <div class="position-relative d-flex flex-row-reverse flex-lg-row flex-wrap flex-lg-nowrap flex-justify-center flex-lg-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light "> - <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0"> - <li class="mr-3 mr-lg-0">© 2019 <span title="0.38259s from unicorn-7478f9985c-skxnd">GitHub</span>, Inc.</li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to security, text:security" href="https://github.com/security">Security</a></li> - <li class="mr-3 mr-lg-0"><a href="https://githubstatus.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li> - </ul> + if strain == "Tc148": + VAPtable = VAP_148 + VAPname='Tc148\nGenome VAP' + if strain == "IL3000": + VAPtable = VAP_IL3000 + VAPname= 'IL3000\nGenome VAP' + width = 0.35 # the width of the bars: can also be len(x) sequence + plots = [] + fpos = 0 + vpos = 0 + for p in range(0, 15): + tp = plt.bar(0, freqList[p], width, color= palette[p], bottom = fpos) + fpos +=freqList[p] + + tp = plt.bar(1, VAPtable[p], width, color= palette[p], bottom = vpos) + vpos +=VAPtable[p] - <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com"> - <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> -</a> - <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0"> - <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li> - <li class="mr-3 mr-lg-0"><a href="https://github.com/pricing" data-ga-click="Footer, go to Pricing, text:Pricing">Pricing</a></li> - <li class="mr-3 mr-lg-0"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li class="mr-3 mr-lg-0"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li class="mr-3 mr-lg-0"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li> + plots.append(tp) + plt.xticks([0,1],[name,VAPname]) + plt.legend(plots[::-1],['p15','p14','p13','p12','p11','p10','p9','p8','p7','p6','p5','p4','p3','p2','p1']) + title = "Figure Legend: The transcriptomic Variant Antigen Profile of $\itTrypanosoma$ $\itcongolense$ estimated as phylotype " \ + "proportion adjusted for transcript abundance and the reference genomic Variant Antigen Profile. " \ + "\nData was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019)." + #plt.title(title, wrap="True") + #plt.text(-0.2, -0.05, title, va="top", transform=ax.transAxes, wrap="True") + plt.text(-0.3, -0.15, title, va="top", wrap="True") + plt.tight_layout(pad=1.5) + plt.subplots_adjust(bottom = 0.3,top=0.99,left=0.125,right=0.9,hspace=0.2,wspace=0.2) - </ul> - </div> - <div class="d-flex flex-justify-center pb-6"> - <span class="f6 text-gray-light"></span> - </div> -</div> - + plt.savefig(html_resource + "/stackedbar.png") + if pdf == 'PDF_Yes': + plt.savefig(html_resource + "/stackedbar.pdf") + #plt.show() - <div id="ajax-error-message" class="ajax-error-message flash flash-error"> - <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg> - <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> - <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> - </button> - You can’t perform that action at this time. - </div> +def createHTML(name,htmlfn,htmlresource,freqList,weightList): + #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource + htmlString = r"<html><title>T.congolense VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma congolense</i> Variant Antigen Profile</h2><h3>" + htmlString += name + htmlString += r"<br>Transcriptomic Analysis</h3></p>" + htmlString += "<p style = 'margin-left:20%; margin-right:20%'>Table Legend: Variant Antigen Profiles of a transcriptome of <i>Trypanosoma congolense</i> estimated as phylotype proportion. " \ + "Weighted frequency refers to the phylotype proportion based transcript abundance. " \ + "Data was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019).</p> " + htmlString += r"<style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style>" + htmlString += r"<table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><th>Relative Frequency</th><th>Weighted Frequency</th></tr>" + tabString = "" + # flush out table with correct values + for i in range(0, 15): + f = format(freqList[i], '.4f') + w = format(weightList[i], '.4f') + tabString += "<tr><td>phy" + str(i + 1) + "</td><td>" + f + "</td><td>" + w + "</td></tr>" + htmlString += tabString + "</table><br><br><br><br><br>" + htmlString += r"<p> <h3>Stacked Bar chart of Phylotype Frequency</h3> The 'weighted' relative frequency of each phylotype alongside the VAP of selected strain.</p>" + imgString = r"<img src = 'stackedbar.png' alt='Stacked bar chart of phylotype variation' style='max-width:100%'><br><br>" + htmlString += imgString + +# htmlString += r"<p><h3>The Deviation Heat Map and Dendogram</h3>The phylotype variation expressed as the deviation from your sample mean compared to the model dataset</p>" +# imgString = r"<img src = 'dheatmap.png' alt='Deviation Heatmap' style='max-width:100%'><br><br>" +# htmlString += imgString + +# htmlString += r"<p><h3>The Variation PCA plot</h3>PCA analysis corresponding to absolute variation. Colour coded according to location</p>" +# imgString = r"<img src = 'vapPCA.png' alt='PCA Analysis' style='max-width:100%'><br><br>" +# htmlString += imgString + r"</div></body></html>" + + with open(htmlfn, "w") as htmlfile: + htmlfile.write(htmlString) - <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script> - <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script> - - <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script> - - - - <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden - > - <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg> - <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span> - <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span> - </div> - <template id="site-details-dialog"> - <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open> - <summary role="button" aria-label="Close dialog"></summary> - <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal"> - <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog> - <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> - </button> - <div class="octocat-spinner my-6 js-details-dialog-spinner"></div> - </details-dialog> - </details> -</template> +#argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} +def transcriptomicProcess(args,dict): + transcriptMapping(args[dict['name']], args[dict['strain']], args[dict['forward']], args[dict['reverse']]) #uses bowtie + processSamFiles(args[dict['name']]) #uses samtools + transcriptAbundance(args[dict['name']],args[dict['strain']]) #uses cufflinks -> ?.cuff/*.* + cuff_df = convertToFasta(args[dict['name']],args[dict['strain']]) + countList, weightList = HMMerMotifSearch(args[dict['name']],args[dict['strain']], cuff_df) + relFreqList = relativeFrequencyTable(countList,args[dict['name']],args[dict['html_resource']]) + relWeightList = weightedFrequencyTable(weightList,args[dict['name']],args[dict['html_resource']]) + createStackedBar(args[dict['name']],relWeightList, args[dict['strain']],args[dict['pdfexport']],args[dict['html_resource']]) + createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']], relFreqList, relWeightList) - <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0"> - <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;"> - </div> -</div> +if __name__ == "__main__": + #print("Commencing Transcript Mapping") + #transcriptMapping("T_Test", "Transcripts.1","Transcripts.2") + #print("Processimg Sam Files") + #processSamFiles("T_Test") + #print("Assessing Transcript Abundance") + #transcriptAbundance("T_Test") + #print ("Converting to Fasta Subset") + #cuff_df = convertToFasta("T_Test") + #print("Commencing HMMer search") + #countList, weightList = HMMerMotifSearch("T_Test",cuff_df) + #relativeFrequencyTable(countList,'T_Test') + #weightedFrequencyTable(weightList,'T_Test') + relFreqList = [0.111842105,0.059210526,0.026315789,0.013157895, + 0.006578947,0.013157895,0.032894737,0.019736842, + 0.039473684,0.046052632,0.217105263,0.065789474, + 0.151315789,0.059210526,0.138157895] - <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div> + relWeightList = [0.07532571,0.05900545,0.009601452,0.042357532,0.01236219,0.001675663,0.04109726, + 0.097464248,0.057491666,0.05826875,0.279457473,0.070004772,0.065329007,0.085361298,0.045197529] - </body> -</html> - + createStackedBar('T_Test',relWeightList, 'Tc148','PDF_Yes','results') + createHTML("t_test","results/t_test.html","results",relFreqList,relWeightList)