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Tryp_T.py |
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| diff -r c4e87b277576 -r 5e346d75ccf3 Tryp_T.py --- a/Tryp_T.py Mon Jun 03 15:58:48 2019 -0400 +++ b/Tryp_T.py Mon Jun 03 15:59:39 2019 -0400 |
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| b'@@ -1,2261 +1,345 @@\n-\n-\n-\n-\n-\n-\n-<!DOCTYPE html>\n-<html lang="en">\n- <head>\n- <meta charset="utf-8">\n- <link rel="dns-prefetch" href="https://github.githubassets.com">\n- <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com">\n- <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com">\n- <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com">\n- <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com">\n- <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com">\n- <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/">\n-\n-\n-\n- <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" />\n- <link crossorigin="anonymous" media="all" 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data-pjax-transient="true" />\n-\n-\n-\n- <m'..b'67 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+#argdict = {\'name\':2, \'pdfexport\': 3, \'strain\': 4, \'forward\': 5, \'reverse\': 6, \'html_file\': 7, \'html_resource\': 8}\n+def transcriptomicProcess(args,dict):\n+ transcriptMapping(args[dict[\'name\']], args[dict[\'strain\']], args[dict[\'forward\']], args[dict[\'reverse\']]) #uses bowtie\n+ processSamFiles(args[dict[\'name\']]) #uses samtools\n+ transcriptAbundance(args[dict[\'name\']],args[dict[\'strain\']]) #uses cufflinks -> ?.cuff/*.*\n+ cuff_df = convertToFasta(args[dict[\'name\']],args[dict[\'strain\']])\n+ countList, weightList = HMMerMotifSearch(args[dict[\'name\']],args[dict[\'strain\']], cuff_df)\n+ relFreqList = relativeFrequencyTable(countList,args[dict[\'name\']],args[dict[\'html_resource\']])\n+ relWeightList = weightedFrequencyTable(weightList,args[dict[\'name\']],args[dict[\'html_resource\']])\n+ createStackedBar(args[dict[\'name\']],relWeightList, args[dict[\'strain\']],args[dict[\'pdfexport\']],args[dict[\'html_resource\']])\n+ createHTML(args[dict[\'name\']],args[dict[\'html_file\']],args[dict[\'html_resource\']], relFreqList, relWeightList)\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+if __name__ == "__main__":\n+ #print("Commencing Transcript Mapping")\n+ #transcriptMapping("T_Test", "Transcripts.1","Transcripts.2")\n+ #print("Processimg Sam Files")\n+ #processSamFiles("T_Test")\n+ #print("Assessing Transcript Abundance")\n+ #transcriptAbundance("T_Test")\n+ #print ("Converting to Fasta Subset")\n+ #cuff_df = convertToFasta("T_Test")\n+ #print("Commencing HMMer search")\n+ #countList, weightList = HMMerMotifSearch("T_Test",cuff_df)\n+ #relativeFrequencyTable(countList,\'T_Test\')\n+ #weightedFrequencyTable(weightList,\'T_Test\')\n+ relFreqList = [0.111842105,0.059210526,0.026315789,0.013157895,\n+ 0.006578947,0.013157895,0.032894737,0.019736842,\n+ 0.039473684,0.046052632,0.217105263,0.065789474,\n+ 0.151315789,0.059210526,0.138157895]\n \n- <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>\n+ relWeightList = [0.07532571,0.05900545,0.009601452,0.042357532,0.01236219,0.001675663,0.04109726,\n+ 0.097464248,0.057491666,0.05826875,0.279457473,0.070004772,0.065329007,0.085361298,0.045197529]\n \n- </body>\n-</html>\n-\n+ createStackedBar(\'T_Test\',relWeightList, \'Tc148\',\'PDF_Yes\',\'results\')\n+ createHTML("t_test","results/t_test.html","results",relFreqList,relWeightList)\n' |