Mercurial > repos > johnheap > vapper
view Vap.py @ 18:e7da2274c9f6 draft
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| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 16:00:24 -0400 |
| parents | c4463e84a7ea |
| children | 26ec953069b3 |
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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"><span class="pl-c"><span class="pl-c">#</span>import subprocess</span></td> </tr> <tr> <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import re</span></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> os</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> sys</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-c"><span class="pl-c">#</span>import pandas as pd</span></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-c"><span class="pl-c">#</span>import numpy as np</span></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-c"><span class="pl-c">#</span>import seaborn as sns</span></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-c"><span class="pl-c">#</span>import matplotlib.pyplot as plt</span></td> </tr> <tr> <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>from matplotlib.mlab import PCA</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> Tryp_G</td> </tr> <tr> <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_T</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"><span class="pl-k">import</span> Tryp_V</td> </tr> <tr> <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V_T</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">import</span> argparse</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>Entry .sort out the arguments</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"> </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">pdfExport <span class="pl-k">=</span> <span class="pl-c1">False</span></td> </tr> <tr> <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.')</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"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('name')</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-c"><span class="pl-c">#</span>parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway")</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"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory")</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>parser.add_argument('strain')</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>parser.add_argument('Forward_Read_File')</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"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('Reverse_Read_File')</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>parser.add_argument('htmlfile')</span></td> </tr> <tr> <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('htmlresource')</span></td> </tr> <tr> <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument('heatmapFile')</span></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-c"><span class="pl-c">#</span>parser.add_argument('PCAFile')</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>parser.add_argument('devheatmapFile')</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>args = parser.parse_args()</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"> </td> </tr> <tr> <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>we have numerous parameters....</span></td> </tr> <tr> <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> <td id="LC51" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>hard code it for differnt types?</span></td> </tr> <tr> <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> <td id="LC52" class="blob-code blob-code-inner js-file-line"> </td> </tr> <tr> <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> <td id="LC53" class="blob-code blob-code-inner js-file-line"> </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">arguments <span class="pl-k">=</span> sys.argv</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">htmldir <span class="pl-k">=</span> arguments[<span class="pl-c1">len</span>(arguments)<span class="pl-k">-</span><span class="pl-c1">1</span>] <span class="pl-c"><span class="pl-c">#</span>last argument is always html_resource</span></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-k">if</span> <span class="pl-k">not</span> os.path.exists(htmldir):</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"> os.mkdir(htmldir)</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"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>g_assemble<span class="pl-pds">'</span></span>:</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"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>kmers<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>,<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>:<span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>:<span class="pl-c1">8</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">9</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">10</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"> Tryp_G.assemble(arguments,argdict)</td> </tr> <tr> <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>g_contigs<span class="pl-pds">'</span></span>:</td> </tr> <tr> <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> <td id="LC63" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">6</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"> Tryp_G.contigs(arguments,argdict)</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-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>transcipt<span class="pl-pds">'</span></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"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>: <span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>strain<span class="pl-pds">'</span></span>: <span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>: <span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>: <span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>: <span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>: <span class="pl-c1">8</span>}</td> </tr> <tr> <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> <td id="LC67" class="blob-code blob-code-inner js-file-line"> Tryp_T.transcriptomicProcess(arguments,argdict)</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"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_assemble<span class="pl-pds">'</span></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"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>kmers<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>,<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>:<span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>:<span class="pl-c1">8</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">9</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">10</span>}</td> </tr> <tr> <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> <td id="LC70" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_assemble(arguments,argdict)</td> </tr> <tr> <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> <td id="LC71" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_contigs<span class="pl-pds">'</span></span>:</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"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>:<span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>:<span class="pl-c1">6</span>}</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"> Tryp_V.vivax_contigs(arguments,argdict)</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"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>v_transcript<span class="pl-pds">'</span></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"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>: <span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>: <span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>: <span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>: <span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>: <span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>: <span class="pl-c1">8</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"> Tryp_V_T.transcriptomicProcess(arguments,argdict)</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"> </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"> </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">sys.exit()</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"> </td> </tr> </table> <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" 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