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Tryp_G.py |
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| diff -r 7f3cfd8d114c -r e91e41380946 Tryp_G.py --- a/Tryp_G.py Mon Jun 03 14:04:16 2019 -0400 +++ b/Tryp_G.py Mon Jun 03 14:05:47 2019 -0400 |
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| b'@@ -1,406 +1,2528 @@\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-import subprocess\r\n-import re\r\n-import os\r\n-import sys\r\n-import shutil\r\n-import pandas as pd\r\n-import numpy as np\r\n-import matplotlib as mpl\r\n-mpl.use(\'Agg\')\r\n-import matplotlib.pyplot as plt\r\n-from matplotlib.mlab import PCA\r\n-import seaborn as sns\r\n-\r\n-# some globals for convenience\r\n-\r\n-pList = [\'P1\', \'P2\', \'P3\', \'P4\', \'P5\', \'P6\', \'P7\', \'P8\', \'P9\', \'P10\', \'P11\', \'P12\', \'P13\', \'P14\', \'P15\']\r\n-\r\n-quietString = ""\t#" >>"+os.path.dirname(os.path.realpath(__file__))+"/log/Vap_log.txt 2>&1"\r\n-\r\n-def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name):\r\n- #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"\r\n- argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name+quietString\r\n- print(argString)\r\n- returncode = subprocess.call(argString, shell=True)\r\n- if returncode != 0:\r\n- return "Error in velveth"\r\n- argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString\r\n- #argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString\r\n- print(argString)\r\n- returncode = subprocess.call(argString, shell = True)\r\n- if returncode != 0:\r\n- return "Error in velvetg"\r\n- shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa") # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";\r\n- return "ok"\r\n-\r\n-def contigTranslation(name):\r\n- argString = "transeq " + name + ".fa " + name + "_6frame.fas -frame=6 " #+quietString\r\n- print(argString)\r\n- returncode = subprocess.call(argString, shell=True)\r\n-\r\n-\r\n-def HMMerMotifSearch(name):\r\n- motifs = [\'1\', \'2a\', \'2b\', \'3\', \'4a\', \'4b\', \'4c\', \'5\', \'6\', \'7\', \'8a\', \'8b\', \'9a\', \'9b\',\r\n- \'9c\', \'10a\', \'10b\', \'11a\', \'11b\', \'12\', \'13a\', \'13b\', \'13c\', \'13d\', \'14\', \'15a\', \'15b\', \'15c\']\r\n- lineCounts = []\r\n- compoundList = []\r\n- dir_path = os.path.dirname(os.path.realpath(__file__))\r\n- phylopath = dir_path + "/data/Motifs/Phylotype"\r\n- for m in motifs:\r\n- argString = "hmmsearch " + phylopath + m + ".hmm " + name + "_6frame.fas > Phy" + m + ".out" # +quietString\r\n- # argString = "hmmsearch "+phylopath + m + ".hmm " + dir_path+"/data/Test_6frame.fas > Phy" + m + ".out"\r\n- #print(argString)\r\n- subprocess.call(argString, shell=True)\r\n-\r\n- hmmResult = open("Phy" + m + ".out", \'r\')\r\n- tempout = open(dir_path + "/data/" + "Phy" + m + ".txt", \'w\')\r\n- #regex = r"NODE_[0-9]{1,7}_length_[0-9]{1,7}_cov_[0-9]{1,10}.[0-9]{1,7}_[0-9]{1,2}"\r\n- n = 0\r\n- outList = []\r\n- for l in range(0,14):\r\n- hmmResult.readline() #hacky? miss out the first 14 lines. data we want starts on line 15\r\n-\r\n-\r\n- for line in hmmResult:\r\n- if re.search(r"inclusion", line):\r\n- #print("inclusion threshold reached")\r\n- break\r\n- if len(line) <= 1:\r\n- #print("end of data")\r\n- '..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' |