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Tryp_T.py |
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| diff -r e91e41380946 -r 25226d33642e Tryp_T.py --- a/Tryp_T.py Mon Jun 03 14:05:47 2019 -0400 +++ b/Tryp_T.py Mon Jun 03 14:06:47 2019 -0400 |
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| b'@@ -1,345 +1,2261 @@\n-"""\r\n- * Copyright 2018 University of Liverpool\r\n- * Author: John Heap, Computational Biology Facility, UoL\r\n- * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL\r\n- *\r\n- * Licensed under the Apache License, Version 2.0 (the "License");\r\n- * you may not use this file except in compliance with the License.\r\n- * You may obtain a copy of the License at\r\n- *\r\n- * http://www.apache.org/licenses/LICENSE-2.0\r\n- *\r\n- * Unless required by applicable law or agreed to in writing, software\r\n- * distributed under the License is distributed on an "AS IS" BASIS,\r\n- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\r\n- * See the License for the specific language governing permissions and\r\n- * limitations under the License.\r\n- *\r\n- """\r\n-\r\n-\r\n-import subprocess\r\n-import pandas as pd\r\n-import re\r\n-import os\r\n-import sys\r\n-import matplotlib as mpl\r\n-mpl.use(\'Agg\')\r\n-import matplotlib.pyplot as plt\r\n-\r\n-pList = [\'P1\', \'P2\', \'P3\', \'P4\', \'P5\', \'P6\', \'P7\', \'P8\', \'P9\', \'P10\', \'P11\', \'P12\', \'P13\', \'P14\', \'P15\']\r\n-quietString = "" #"">> Vap_log.txt 2>&1"\r\n-def transcriptMapping(inputname, strain, forwardFN,reverseFN):\r\n- #where is our Reference data -\r\n- dir_path = os.path.dirname(os.path.realpath(__file__))\r\n- refName = dir_path+"/data/Reference/Tc148" #default\r\n- if strain == "Tc148":\r\n- refName = dir_path+"/data/Reference/Tc148"\r\n- if strain == "IL3000":\r\n- refName = dir_path+"/data/Reference/IL3000"\r\n- #argString = "bowtie2 -x Refe4rence/IL3000 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt\r\n- #argString = "bowtie2 -x Reference/Tc148 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt\r\n- argString = "bowtie2 -x "+refName+" -1 "+forwardFN+" -2 "+reverseFN+" -S "+inputname+".sam"+quietString #>log.txt\r\n- #print(argString)\r\n- returncode = subprocess.call(argString, shell=True)\r\n-\r\n-def processSamFiles(inputname):\r\n- #debug use a mapping sam file we have already found\r\n- #dir_path = os.path.dirname(os.path.realpath(__file__))\r\n- #bugName = dir_path+"/data/T_Test" #defasult\r\n-\r\n- cur_path = os.getcwd()\r\n- samName = cur_path+"/"+inputname\r\n-\r\n- #argString = "samtools view -bS "+bugName+" > "+inputname+".bam"\r\n- argString = "samtools view -bS "+inputname+".sam > "+samName+".bam"+quietString\r\n- #print(argString)\r\n- returncode = subprocess.call(argString, shell=True)\r\n-\r\n-\r\n- #argString = "samtools sort "+bugName+" -o "+inputname+".sorted"\r\n- argString = "samtools sort "+samName+".bam -o "+samName+".sorted"+quietString\r\n- #print("argstring = "+argString)\r\n- returncode = subprocess.call(argString, shell=True)\r\n-\r\n- #argString = "samtools index "+bugName+".sorted "+inputname+".sorted.bai"\r\n- argString = "samtools index "+samName+".sorted "+samName+".sorted.bai"+quietString\r\n- #print("argstring = " + argString)\r\n- returncode = subprocess.call(argString, shell=True)\r\n-\r\n-\r\n-\r\n-\r\n-def transcriptAbundance(inputname, strain):\r\n- dir_path = os.path.dirname(os.path.realpath(__file__))\r\n- refName = dir_path + "/data/Reference/ORFAnnotation.gtf" # defasult\r\n- if strain == "Tc148":\r\n- refName = dir_path + "/data/Reference/ORFAnnotation.gtf"\r\n- if strain == "IL3000":\r\n- refName = dir_path + "/data/Reference/IL3000.gtf"\r\n- #argString = "cufflinks -G Reference/IL3000.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"\r\n- #argString = "cufflinks -G Reference/ORFAnnotation.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"\r\n- argString = "cufflinks -q -G "+refName+" -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"+quietString\r\n- returncode = subprocess.call(argString, shell = True)\r\n-\r\n-\r\n-def convertToFasta(inputName, strain): #equivalent to Sara\'s awk scripte\r\n- dir_path = os.path.dirname(os.path.realpath(__file__))\r\n- refName = dir_path + "/data/Reference/ORFAnnotation.'..b'a-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>\n+\n+ </ul>\n+ </div>\n+ <div class="d-flex flex-justify-center pb-6">\n+ <span class="f6 text-gray-light"></span>\n+ </div>\n+</div>\n+\n+\n+\n+ <div id="ajax-error-message" class="ajax-error-message flash flash-error">\n+ <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>\n+ <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">\n+ <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>\n+ </button>\n+ You can\xe2\x80\x99t perform that action at this time.\n+ </div>\n+\n+\n+ <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>\n+ <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>\n+ \n+ <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script>\n+ \n+ \n+ \n+ <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden\n+ >\n+ <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>\n+ <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>\n+ <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>\n+ </div>\n+ <template id="site-details-dialog">\n+ <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>\n+ <summary role="button" aria-label="Close dialog"></summary>\n+ <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">\n+ <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>\n+ <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>\n+ </button>\n+ <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>\n+ </details-dialog>\n+ </details>\n+</template>\n+\n+ <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">\n+ <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">\n+ </div>\n+</div>\n+\n+ <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>\n+\n+ </body>\n+</html>\n+\n' |