Mercurial > repos > johnheap > vapper
comparison Tryp_T.py @ 17:5e346d75ccf3 draft
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author | johnheap |
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date | Mon, 03 Jun 2019 15:59:39 -0400 |
parents | 25226d33642e |
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16:c4e87b277576 | 17:5e346d75ccf3 |
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1 | 1 """ |
2 | 2 * Copyright 2018 University of Liverpool |
3 | 3 * Author: John Heap, Computational Biology Facility, UoL |
4 | 4 * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL |
5 | 5 * |
6 | 6 * Licensed under the Apache License, Version 2.0 (the "License"); |
7 <!DOCTYPE html> | 7 * you may not use this file except in compliance with the License. |
8 <html lang="en"> | 8 * You may obtain a copy of the License at |
9 <head> | 9 * |
10 <meta charset="utf-8"> | 10 * http://www.apache.org/licenses/LICENSE-2.0 |
11 <link rel="dns-prefetch" href="https://github.githubassets.com"> | 11 * |
12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> | 12 * Unless required by applicable law or agreed to in writing, software |
13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> | 13 * distributed under the License is distributed on an "AS IS" BASIS, |
14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> | 14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> | 15 * See the License for the specific language governing permissions and |
16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> | 16 * limitations under the License. |
17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> | 17 * |
18 | 18 """ |
19 | 19 |
20 | 20 |
21 <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" /> | 21 import subprocess |
22 <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" /> | 22 import pandas as pd |
23 <link crossorigin="anonymous" media="all" integrity="sha512-XjvAy/mMWN5aOA+pyb/FgAgcVgJkPkwTCwvFK07Ez/H44lvl55ZLGwtpyL4MaMrwDE8QYO+1VYljKFjqr4/iJA==" rel="stylesheet" href="https://github.githubassets.com/assets/github-5b066aa36cc405c9cbcbadf1bde399ed.css" /> | 23 import re |
24 | 24 import os |
25 | 25 import sys |
26 | 26 import matplotlib as mpl |
27 | 27 mpl.use('Agg') |
28 | 28 import matplotlib.pyplot as plt |
29 <meta name="viewport" content="width=device-width"> | 29 |
30 | 30 pList = ['P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'P9', 'P10', 'P11', 'P12', 'P13', 'P14', 'P15'] |
31 <title>VAPPER-Galaxy/Tryp_T.py at master · johnheap/VAPPER-Galaxy · GitHub</title> | 31 quietString = "" #"">> Vap_log.txt 2>&1" |
32 <meta name="description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub."> | 32 def transcriptMapping(inputname, strain, forwardFN,reverseFN): |
33 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> | 33 #where is our Reference data - |
34 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> | 34 dir_path = os.path.dirname(os.path.realpath(__file__)) |
35 <meta property="fb:app_id" content="1401488693436528"> | 35 refName = dir_path+"/data/Reference/Tc148" #default |
36 | 36 if strain == "Tc148": |
37 <meta name="twitter:image:src" content="https://avatars0.githubusercontent.com/u/24318980?s=400&v=4" /><meta name="twitter:site" content="@github" /><meta name="twitter:card" content="summary" /><meta name="twitter:title" content="johnheap/VAPPER-Galaxy" /><meta name="twitter:description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub." /> | 37 refName = dir_path+"/data/Reference/Tc148" |
38 <meta property="og:image" content="https://avatars0.githubusercontent.com/u/24318980?s=400&v=4" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="johnheap/VAPPER-Galaxy" /><meta property="og:url" content="https://github.com/johnheap/VAPPER-Galaxy" /><meta property="og:description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub." /> | 38 if strain == "IL3000": |
39 | 39 refName = dir_path+"/data/Reference/IL3000" |
40 <link rel="assets" href="https://github.githubassets.com/"> | 40 #argString = "bowtie2 -x Refe4rence/IL3000 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt |
41 | 41 #argString = "bowtie2 -x Reference/Tc148 -1 data/"+forwardFN+" -2 data/"+reverseFN+" -S "+inputname+".sam" #>log.txt |
42 <meta name="pjax-timeout" content="1000"> | 42 argString = "bowtie2 -x "+refName+" -1 "+forwardFN+" -2 "+reverseFN+" -S "+inputname+".sam"+quietString #>log.txt |
43 | 43 #print(argString) |
44 <meta name="request-id" content="A68B:03C7:99543:10DBF9:5CF561B6" data-pjax-transient> | 44 returncode = subprocess.call(argString, shell=True) |
45 | 45 |
46 | 46 def processSamFiles(inputname): |
47 | 47 #debug use a mapping sam file we have already found |
48 | 48 #dir_path = os.path.dirname(os.path.realpath(__file__)) |
49 <meta name="selected-link" value="repo_source" data-pjax-transient> | 49 #bugName = dir_path+"/data/T_Test" #defasult |
50 | 50 |
51 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> | 51 cur_path = os.getcwd() |
52 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> | 52 samName = cur_path+"/"+inputname |
53 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc"> | 53 |
54 | 54 #argString = "samtools view -bS "+bugName+" > "+inputname+".bam" |
55 <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="A68B:03C7:99543:10DBF9:5CF561B6" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" /> | 55 argString = "samtools view -bS "+inputname+".sam > "+samName+".bam"+quietString |
56 <meta name="analytics-location" content="/<user-name>/<repo-name>/blob/show" data-pjax-transient="true" /> | 56 #print(argString) |
57 | 57 returncode = subprocess.call(argString, shell=True) |
58 | 58 |
59 | 59 |
60 <meta name="google-analytics" content="UA-3769691-2"> | 60 #argString = "samtools sort "+bugName+" -o "+inputname+".sorted" |
61 | 61 argString = "samtools sort "+samName+".bam -o "+samName+".sorted"+quietString |
62 | 62 #print("argstring = "+argString) |
63 <meta class="js-ga-set" name="dimension1" content="Logged Out"> | 63 returncode = subprocess.call(argString, shell=True) |
64 | 64 |
65 | 65 #argString = "samtools index "+bugName+".sorted "+inputname+".sorted.bai" |
66 | 66 argString = "samtools index "+samName+".sorted "+samName+".sorted.bai"+quietString |
67 | 67 #print("argstring = " + argString) |
68 | 68 returncode = subprocess.call(argString, shell=True) |
69 <meta name="hostname" content="github.com"> | 69 |
70 <meta name="user-login" content=""> | 70 |
71 | 71 |
72 <meta name="expected-hostname" content="github.com"> | 72 |
73 <meta name="js-proxy-site-detection-payload" content="MzM5YjY3ZjNjYzY5Y2RhNDI5MDYxM2MzZTc0ZGExYzUxM2I3NjhiNTdmNGE2NjMwYWVjMzFhMGIzNWY0MDU3OHx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiJBNjhCOjAzQzc6OTk1NDM6MTBEQkY5OjVDRjU2MUI2IiwidGltZXN0YW1wIjoxNTU5NTg1MjA3LCJob3N0IjoiZ2l0aHViLmNvbSJ9"> | 73 def transcriptAbundance(inputname, strain): |
74 | 74 dir_path = os.path.dirname(os.path.realpath(__file__)) |
75 <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS"> | 75 refName = dir_path + "/data/Reference/ORFAnnotation.gtf" # defasult |
76 | 76 if strain == "Tc148": |
77 <meta name="html-safe-nonce" content="632a90d8ff46863b6a26a12d9d6ed92a6679abbf"> | 77 refName = dir_path + "/data/Reference/ORFAnnotation.gtf" |
78 | 78 if strain == "IL3000": |
79 <meta http-equiv="x-pjax-version" content="af1499c2254d0582d0a98af1dfd7f11b"> | 79 refName = dir_path + "/data/Reference/IL3000.gtf" |
80 | 80 #argString = "cufflinks -G Reference/IL3000.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted" |
81 | 81 #argString = "cufflinks -G Reference/ORFAnnotation.gtf -o "+inputname+".cuff -u -p 8 "+inputname+".sorted" |
82 <link href="https://github.com/johnheap/VAPPER-Galaxy/commits/master.atom" rel="alternate" title="Recent Commits to VAPPER-Galaxy:master" type="application/atom+xml"> | 82 argString = "cufflinks -q -G "+refName+" -o "+inputname+".cuff -u -p 8 "+inputname+".sorted"+quietString |
83 | 83 returncode = subprocess.call(argString, shell = True) |
84 <meta name="go-import" content="github.com/johnheap/VAPPER-Galaxy git https://github.com/johnheap/VAPPER-Galaxy.git"> | 84 |
85 | 85 |
86 <meta name="octolytics-dimension-user_id" content="24318980" /><meta name="octolytics-dimension-user_login" content="johnheap" /><meta name="octolytics-dimension-repository_id" content="139730674" /><meta name="octolytics-dimension-repository_nwo" content="johnheap/VAPPER-Galaxy" /><meta name="octolytics-dimension-repository_public" content="true" /><meta name="octolytics-dimension-repository_is_fork" content="false" /><meta name="octolytics-dimension-repository_network_root_id" content="139730674" /><meta name="octolytics-dimension-repository_network_root_nwo" content="johnheap/VAPPER-Galaxy" /><meta name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" content="false" /> | 86 def convertToFasta(inputName, strain): #equivalent to Sara's awk scripte |
87 | 87 dir_path = os.path.dirname(os.path.realpath(__file__)) |
88 | 88 refName = dir_path + "/data/Reference/ORFAnnotation.gtf" # default |
89 <link rel="canonical" href="https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py" data-pjax-transient> | 89 if strain == "Tc148": |
90 | 90 refName = dir_path + "/data/Reference/148_prot.fasta" |
91 | 91 if strain == "IL3000": |
92 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats"> | 92 refName = dir_path + "/data/Reference/IL3000_prot.fasta" |
93 | 93 |
94 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors"> | 94 cuff_df = pd.read_csv(inputName+".cuff/genes.fpkm_tracking", sep='\t') |
95 | 95 cuff_df = cuff_df[(cuff_df['FPKM'] > 0)] |
96 <link rel="mask-icon" href="https://github.githubassets.com/pinned-octocat.svg" color="#000000"> | 96 cuff_df.to_csv("cuffTest.csv") |
97 <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://github.githubassets.com/favicon.ico"> | 97 gene_id_List = cuff_df['gene_id'].tolist() |
98 | 98 |
99 <meta name="theme-color" content="#1e2327"> | 99 #print(gene_id_List) |
100 | 100 #print ("Found from 8880="+str(found)) |
101 | 101 |
102 | 102 # need to load in IL3000_prot.fasta |
103 | 103 # for each line with >TcIL3000_1_1940 |
104 | 104 # search within cuff_df[gene_id] for match |
105 <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials"> | 105 # add it to the outfile. (need to save it as used by hmmer later |
106 | 106 number = 0 |
107 </head> | 107 all = 0 |
108 | 108 with open(inputName+"_6frame.fas", 'w') as outfile: |
109 <body class="logged-out env-production page-responsive page-blob"> | 109 ref = open(refName,'r') |
110 | 110 #ref = open(r"Reference/IL3000_prot.fasta",'r') |
111 | 111 n = 0 |
112 <div class="position-relative js-header-wrapper "> | 112 line = ref.readline() |
113 <a href="#start-of-content" tabindex="1" class="px-2 py-4 bg-blue text-white show-on-focus js-skip-to-content">Skip to content</a> | 113 while line: |
114 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div> | 114 if line[0] == '>': |
115 | 115 all = all+1 |
116 | 116 ln = line[1:] #remove > |
117 | 117 ln = ln.rstrip() #remove /n /r etc |
118 | 118 #print (ln) |
119 | 119 if ln in gene_id_List: |
120 | 120 number = number+1 |
121 <header class="Header-old header-logged-out js-details-container Details position-relative f4 py-2" role="banner"> | 121 outfile.write(line) |
122 <div class="container-lg d-lg-flex flex-items-center p-responsive"> | 122 line = ref.readline() |
123 <div class="d-flex flex-justify-between flex-items-center"> | 123 if line: |
124 <a class="mr-4" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark"> | 124 while line[0] != '>': |
125 <svg height="32" class="octicon octicon-mark-github text-white" viewBox="0 0 16 16" version="1.1" width="32" 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> | 125 outfile.write(line) |
126 </a> | 126 line=ref.readline() |
127 | 127 if not line: |
128 <div class="d-lg-none css-truncate css-truncate-target width-fit p-2"> | 128 break; |
129 | 129 else: |
130 <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><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> | 130 line = ref.readline() |
131 <a class="Header-link" href="/johnheap">johnheap</a> | 131 else: |
132 / | 132 line =ref.readline() |
133 <a class="Header-link" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a> | 133 ref.close() |
134 | 134 print(str(len(gene_id_List))+":"+str(number)+" from "+str(all)) |
135 | 135 return cuff_df |
136 </div> | 136 |
137 | 137 def HMMerMotifSearch(name, strain, cuff_df): |
138 <div class="d-flex flex-items-center"> | 138 motifs = ['1', '2a', '2b', '3', '4a', '4b', '4c', '5', '6', '7', '8a', '8b', '9a', '9b', |
139 <a class="d-inline-block d-lg-none f5 text-white no-underline border border-gray-dark rounded-2 px-2 py-1 mr-3 mr-sm-5" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header","repository_id":null,"auth_type":"SIGN_UP","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="2815673fe800ea60b3399372453cd6ad235f12180cead78fa9534b2f8d8e77a5" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo"> | 139 '9c', '10a', '10b', '11a', '11b', '12', '13a', '13b', '13c', '13d', '14', '15a', '15b', '15c'] |
140 Sign up | 140 dir_path = os.path.dirname(os.path.realpath(__file__)) |
141 </a> | 141 phylopath = dir_path + "/data/Motifs/Phylotype" |
142 <button class="btn-link d-lg-none mt-1 js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false"> | 142 lineCounts = [] |
143 <svg height="24" class="octicon octicon-three-bars text-white" viewBox="0 0 12 16" version="1.1" width="18" aria-hidden="true"><path fill-rule="evenodd" d="M11.41 9H.59C0 9 0 8.59 0 8c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zm0-4H.59C0 5 0 4.59 0 4c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zM.59 11H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1H.59C0 13 0 12.59 0 12c0-.59 0-1 .59-1z"/></svg> | 143 compoundList = [] |
144 </button> | 144 for m in motifs: |
145 </div> | 145 argString = "hmmsearch "+phylopath + m + ".hmm " + name + "_6frame.fas > Phy" + m + ".out" |
146 </div> | 146 print(argString) |
147 | 147 subprocess.call(argString, shell=True) |
148 <div class="HeaderMenu HeaderMenu--logged-out position-fixed top-0 right-0 bottom-0 height-fit position-lg-relative d-lg-flex flex-justify-between flex-items-center flex-auto"> | 148 hmmResult = open("Phy" + m + ".out", 'r') |
149 <div class="d-flex d-lg-none flex-justify-end border-bottom bg-gray-light p-3"> | 149 regex = r"Tc148[0-9]{1,8}" |
150 <button class="btn-link js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false"> | 150 if strain == "Tc148": |
151 <svg height="24" class="octicon octicon-x text-gray" viewBox="0 0 12 16" version="1.1" width="18" 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> | 151 regex = r"Tc148[0-9]{1,8}" |
152 </button> | 152 if strain == "IL3000": |
153 </div> | 153 regex = r"TcIL3000_[0-9]{1,4}_[0-9]{1,5}" |
154 | 154 n = 0 |
155 <nav class="mt-0 px-3 px-lg-0 mb-5 mb-lg-0" aria-label="Global"> | 155 outList = [] |
156 <ul class="d-lg-flex list-style-none"> | 156 for line in hmmResult: |
157 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> | 157 m = re.search(regex, line) |
158 <details class="HeaderMenu-details details-overlay details-reset width-full"> | 158 if m: |
159 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> | 159 outList.append(""+m.group()) |
160 Why GitHub? | 160 n += 1 |
161 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> | 161 if re.search(r"inclusion", line): |
162 <path d="M1,1l6.2,6L13,1"></path> | 162 print("inclusion threshold reached") |
163 </svg> | 163 break |
164 </summary> | 164 compoundList.append(outList) |
165 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> | 165 lineCounts.append(n) |
166 <a href="/features" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Features">Features <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a> | 166 hmmResult.close() |
167 <ul class="list-style-none f5 pb-3"> | 167 #print(lineCounts) |
168 <li class="edge-item-fix"><a href="/features/code-review/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code review">Code review</a></li> | 168 |
169 <li class="edge-item-fix"><a href="/features/project-management/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Project management">Project management</a></li> | 169 #print(cuff_df) |
170 <li class="edge-item-fix"><a href="/features/integrations" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Integrations">Integrations</a></li> | 170 concatGroups = [1, 2, 1, 3, 1, 1, 1, 2, 3, 2, 2, 1, 4, 1, 3] |
171 <li class="edge-item-fix"><a href="/features/actions" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Actions">Actions</a> | 171 countList = [] |
172 <li class="edge-item-fix"><a href="/features/package-registry" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Package Registry">Package registry</a> | 172 weightList = [] |
173 <li class="edge-item-fix"><a href="/features#team-management" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Team management">Team management</a></li> | 173 countIndex = 0 |
174 <li class="edge-item-fix"><a href="/features#social-coding" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Social coding">Social coding</a></li> | 174 totalCount = 0 |
175 <li class="edge-item-fix"><a href="/features#documentation" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Documentation">Documentation</a></li> | 175 totalWeigth = 0 |
176 <li class="edge-item-fix"><a href="/features#code-hosting" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code hosting">Code hosting</a></li> | 176 for c in concatGroups: |
177 </ul> | 177 a = [] |
178 | 178 weight = [] |
179 <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> | 179 for n in range(0, c): |
180 <li class="edge-item-fix"><a href="/customer-stories" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Customer stories">Customer stories <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> | 180 a = a + compoundList.pop(0) |
181 <li class="edge-item-fix"><a href="/security" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Security">Security <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> | 181 t = set(a) |
182 </ul> | 182 countList.append(len(t)) |
183 </div> | 183 wa = 0 |
184 </details> | 184 for w in t: |
185 </li> | 185 wt = cuff_df.loc[cuff_df['gene_id'] == w, 'FPKM'].iloc[0] |
186 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> | 186 #print(w) |
187 <a href="/enterprise" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Enterprise">Enterprise</a> | 187 #print(wt) |
188 </li> | 188 wa = wa+wt |
189 | 189 weightList.append(wa) |
190 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> | 190 totalWeigth+=wa |
191 <details class="HeaderMenu-details details-overlay details-reset width-full"> | 191 totalCount += len(t) |
192 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> | 192 countList.append(totalCount) |
193 Explore | 193 weightList.append(totalWeigth) |
194 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> | 194 #print(countList) |
195 <path d="M1,1l6.2,6L13,1"></path> | 195 #print("--------") |
196 </svg> | 196 #print(weightList) |
197 </summary> | 197 #print("--------") |
198 | 198 return countList,weightList |
199 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> | 199 |
200 <ul class="list-style-none mb-3"> | 200 def relativeFrequencyTable(countList, name, htmlresource): |
201 <li class="edge-item-fix"><a href="/explore" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Explore">Explore GitHub <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> | 201 relFreqList = [] |
202 </ul> | 202 c = float(countList[15]) |
203 | 203 for i in range(0, 15): |
204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn & contribute</h4> | 204 relFreqList.append(countList[i] / c) |
205 <ul class="list-style-none mb-3"> | 205 |
206 <li class="edge-item-fix"><a href="/topics" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Topics">Topics</a></li> | 206 data = {'Phylotype': pList, 'Relative Frequency': relFreqList} |
207 <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li> | 207 relFreq_df = pd.DataFrame(data) |
208 <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li> | 208 j_fname = htmlresource+ "/" + name + "_t_relative_frequency.csv" |
209 <li class="edge-item-fix"><a href="https://lab.github.com/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Learning lab">Learning Lab</a></li> | 209 relFreq_df.to_csv(j_fname) |
210 <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li> | 210 return relFreqList # 0-14 = p1-p15 counts [15] = total counts |
211 </ul> | 211 |
212 | 212 |
213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4> | 213 def weightedFrequencyTable(countList, name, htmlresource): |
214 <ul class="list-style-none mb-0"> | 214 relFreqList = [] |
215 <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li> | 215 c = float(countList[15]) |
216 <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li> | 216 for i in range(0, 15): |
217 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li> | 217 relFreqList.append(countList[i] / c) |
218 </ul> | 218 |
219 </div> | 219 data = {'Phylotype': pList, 'Weighted Frequency': relFreqList} |
220 </details> | 220 relFreq_df = pd.DataFrame(data) |
221 </li> | 221 j_fname = htmlresource+ "/" + name + "_t_weighted_frequency.csv" |
222 | 222 relFreq_df.to_csv(j_fname) |
223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> | 223 return relFreqList # 0-14 = p1-p15 counts [15] = total counts |
224 <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a> | 224 |
225 </li> | 225 |
226 | 226 |
227 <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> | 227 def createStackedBar(name,freqList,strain,pdf,html_resource): |
228 <details class="HeaderMenu-details details-overlay details-reset width-full"> | 228 palette = ["#0000ff", "#6495ed", "#00ffff", "#caff70", |
229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> | 229 "#228b22", "#528b8b", "#00ff00", "#a52a2a", |
230 Pricing | 230 "#ff0000", "#ffff00", "#ffa500", "#ff1493", |
231 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> | 231 "#9400d3", "#bebebe", "#000000", "#ff00ff"] |
232 <path d="M1,1l6.2,6L13,1"></path> | 232 |
233 </svg> | 233 VAP_148 = [0.072, 0.032, 0.032, 0.004, 0.007, |
234 </summary> | 234 0.005, 0.202, 0.004, 0.006, 0.014, |
235 | 235 0.130, 0.133, 0.054, 0.039, 0.265] |
236 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> | 236 |
237 <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a> | 237 VAP_IL3000 = [0.073, 0.040, 0.049, 0.018, 0.060, |
238 | 238 0.055, 0.054, 0.025, 0.012, 0.060, |
239 <ul class="list-style-none mb-3"> | 239 0.142, 0.100, 0.061, 0.078, 0.172] |
240 <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li> | 240 cmap = plt.cm.get_cmap('tab20') |
241 <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li> | 241 palette = [cmap(i) for i in range(cmap.N)] |
242 </ul> | 242 |
243 | 243 if strain == "Tc148": |
244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> | 244 VAPtable = VAP_148 |
245 <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> | 245 VAPname='Tc148\nGenome VAP' |
246 <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> | 246 if strain == "IL3000": |
247 </ul> | 247 VAPtable = VAP_IL3000 |
248 </div> | 248 VAPname= 'IL3000\nGenome VAP' |
249 </details> | 249 width = 0.35 # the width of the bars: can also be len(x) sequence |
250 </li> | 250 plots = [] |
251 </ul> | 251 fpos = 0 |
252 </nav> | 252 vpos = 0 |
253 | 253 for p in range(0, 15): |
254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left"> | 254 tp = plt.bar(0, freqList[p], width, color= palette[p], bottom = fpos) |
255 <div class="d-lg-flex mb-3 mb-lg-0"> | 255 fpos +=freqList[p] |
256 <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" | 256 |
257 role="combobox" | 257 tp = plt.bar(1, VAPtable[p], width, color= palette[p], bottom = vpos) |
258 aria-owns="jump-to-results" | 258 vpos +=VAPtable[p] |
259 aria-label="Search or jump to" | 259 |
260 aria-haspopup="listbox" | 260 plots.append(tp) |
261 aria-expanded="false" | 261 plt.xticks([0,1],[name,VAPname]) |
262 > | 262 plt.legend(plots[::-1],['p15','p14','p13','p12','p11','p10','p9','p8','p7','p6','p5','p4','p3','p2','p1']) |
263 <div class="position-relative"> | 263 title = "Figure Legend: The transcriptomic Variant Antigen Profile of $\itTrypanosoma$ $\itcongolense$ estimated as phylotype " \ |
264 <!-- '"` --><!-- </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="✓" /> | 264 "proportion adjusted for transcript abundance and the reference genomic Variant Antigen Profile. " \ |
265 <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"> | 265 "\nData was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019)." |
266 <input type="text" | 266 #plt.title(title, wrap="True") |
267 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" | 267 #plt.text(-0.2, -0.05, title, va="top", transform=ax.transAxes, wrap="True") |
268 data-hotkey="s,/" | 268 plt.text(-0.3, -0.15, title, va="top", wrap="True") |
269 name="q" | 269 plt.tight_layout(pad=1.5) |
270 value="" | 270 plt.subplots_adjust(bottom = 0.3,top=0.99,left=0.125,right=0.9,hspace=0.2,wspace=0.2) |
271 placeholder="Search" | 271 |
272 data-unscoped-placeholder="Search GitHub" | 272 plt.savefig(html_resource + "/stackedbar.png") |
273 data-scoped-placeholder="Search" | 273 if pdf == 'PDF_Yes': |
274 autocapitalize="off" | 274 plt.savefig(html_resource + "/stackedbar.pdf") |
275 aria-autocomplete="list" | 275 #plt.show() |
276 aria-controls="jump-to-results" | 276 |
277 aria-label="Search" | 277 |
278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=aIF6VlsMjmBGKiH9gFW0N7Dd6tKGBfaVG4YIMScDT9WHVDbYUTh6gnqmb9yMT8saP+1TzsRaVWx++i39m514Bw==" | 278 def createHTML(name,htmlfn,htmlresource,freqList,weightList): |
279 spellcheck="false" | 279 #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource |
280 autocomplete="off" | 280 htmlString = r"<html><title>T.congolense VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma congolense</i> Variant Antigen Profile</h2><h3>" |
281 > | 281 htmlString += name |
282 <input type="hidden" class="js-site-search-type-field" name="type" > | 282 htmlString += r"<br>Transcriptomic Analysis</h3></p>" |
283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> | 283 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. " \ |
284 | 284 "Weighted frequency refers to the phylotype proportion based transcript abundance. " \ |
285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> | 285 "Data was produced with the 'Variant Antigen Profiler' (Silva Pereira et al., 2019).</p> " |
286 | 286 htmlString += r"<style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style>" |
287 <ul class="d-none js-jump-to-suggestions-template-container"> | 287 |
288 | 288 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>" |
289 | 289 tabString = "" |
290 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> | 290 # flush out table with correct values |
291 <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=""> | 291 for i in range(0, 15): |
292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> | 292 f = format(freqList[i], '.4f') |
293 <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> | 293 w = format(weightList[i], '.4f') |
294 <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> | 294 tabString += "<tr><td>phy" + str(i + 1) + "</td><td>" + f + "</td><td>" + w + "</td></tr>" |
295 <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> | 295 htmlString += tabString + "</table><br><br><br><br><br>" |
296 </div> | 296 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>" |
297 | 297 imgString = r"<img src = 'stackedbar.png' alt='Stacked bar chart of phylotype variation' style='max-width:100%'><br><br>" |
298 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> | 298 htmlString += imgString |
299 | 299 |
300 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> | 300 # 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>" |
301 </div> | 301 # imgString = r"<img src = 'dheatmap.png' alt='Deviation Heatmap' style='max-width:100%'><br><br>" |
302 | 302 # htmlString += imgString |
303 <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"> | 303 |
304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> | 304 # htmlString += r"<p><h3>The Variation PCA plot</h3>PCA analysis corresponding to absolute variation. Colour coded according to location</p>" |
305 In this repository | 305 # imgString = r"<img src = 'vapPCA.png' alt='PCA Analysis' style='max-width:100%'><br><br>" |
306 </span> | 306 # htmlString += imgString + r"</div></body></html>" |
307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> | 307 |
308 All GitHub | 308 with open(htmlfn, "w") as htmlfile: |
309 </span> | 309 htmlfile.write(htmlString) |
310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> | 310 |
311 </div> | 311 #argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} |
312 | 312 def transcriptomicProcess(args,dict): |
313 <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"> | 313 transcriptMapping(args[dict['name']], args[dict['strain']], args[dict['forward']], args[dict['reverse']]) #uses bowtie |
314 Jump to | 314 processSamFiles(args[dict['name']]) #uses samtools |
315 <span class="d-inline-block ml-1 v-align-middle">↵</span> | 315 transcriptAbundance(args[dict['name']],args[dict['strain']]) #uses cufflinks -> ?.cuff/*.* |
316 </div> | 316 cuff_df = convertToFasta(args[dict['name']],args[dict['strain']]) |
317 </a> | 317 countList, weightList = HMMerMotifSearch(args[dict['name']],args[dict['strain']], cuff_df) |
318 </li> | 318 relFreqList = relativeFrequencyTable(countList,args[dict['name']],args[dict['html_resource']]) |
319 | 319 relWeightList = weightedFrequencyTable(weightList,args[dict['name']],args[dict['html_resource']]) |
320 </ul> | 320 createStackedBar(args[dict['name']],relWeightList, args[dict['strain']],args[dict['pdfexport']],args[dict['html_resource']]) |
321 | 321 createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']], relFreqList, relWeightList) |
322 <ul class="d-none js-jump-to-no-results-template-container"> | 322 |
323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> | 323 if __name__ == "__main__": |
324 <span class="text-gray">No suggested jump to results</span> | 324 #print("Commencing Transcript Mapping") |
325 </li> | 325 #transcriptMapping("T_Test", "Transcripts.1","Transcripts.2") |
326 </ul> | 326 #print("Processimg Sam Files") |
327 | 327 #processSamFiles("T_Test") |
328 <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"> | 328 #print("Assessing Transcript Abundance") |
329 | 329 #transcriptAbundance("T_Test") |
330 | 330 #print ("Converting to Fasta Subset") |
331 <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"> | 331 #cuff_df = convertToFasta("T_Test") |
332 <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=""> | 332 #print("Commencing HMMer search") |
333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> | 333 #countList, weightList = HMMerMotifSearch("T_Test",cuff_df) |
334 <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> | 334 #relativeFrequencyTable(countList,'T_Test') |
335 <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> | 335 #weightedFrequencyTable(weightList,'T_Test') |
336 <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> | 336 relFreqList = [0.111842105,0.059210526,0.026315789,0.013157895, |
337 </div> | 337 0.006578947,0.013157895,0.032894737,0.019736842, |
338 | 338 0.039473684,0.046052632,0.217105263,0.065789474, |
339 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> | 339 0.151315789,0.059210526,0.138157895] |
340 | 340 |
341 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> | 341 relWeightList = [0.07532571,0.05900545,0.009601452,0.042357532,0.01236219,0.001675663,0.04109726, |
342 </div> | 342 0.097464248,0.057491666,0.05826875,0.279457473,0.070004772,0.065329007,0.085361298,0.045197529] |
343 | 343 |
344 <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"> | 344 createStackedBar('T_Test',relWeightList, 'Tc148','PDF_Yes','results') |
345 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> | 345 createHTML("t_test","results/t_test.html","results",relFreqList,relWeightList) |
346 In this repository | |
347 </span> | |
348 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> | |
349 All GitHub | |
350 </span> | |
351 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> | |
352 </div> | |
353 | |
354 <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"> | |
355 Jump to | |
356 <span class="d-inline-block ml-1 v-align-middle">↵</span> | |
357 </div> | |
358 </a> | |
359 </li> | |
360 | |
361 | |
362 | |
363 <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"> | |
364 <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=""> | |
365 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> | |
366 <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> | |
367 <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> | |
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369 </div> | |
370 | |
371 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> | |
372 | |
373 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> | |
374 </div> | |
375 | |
376 <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"> | |
377 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> | |
378 In this repository | |
379 </span> | |
380 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> | |
381 All GitHub | |
382 </span> | |
383 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> | |
384 </div> | |
385 | |
386 <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"> | |
387 Jump to | |
388 <span class="d-inline-block ml-1 v-align-middle">↵</span> | |
389 </div> | |
390 </a> | |
391 </li> | |
392 | |
393 | |
394 </ul> | |
395 | |
396 </div> | |
397 </label> | |
398 </form> </div> | |
399 </div> | |
400 | |
401 </div> | |
402 | |
403 <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"> | |
404 Sign in | |
405 </a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","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="ff072ec41895d40692c4e40554c544f4e6d3a197b0aa2bc35ed34ef5987a3ec2" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo"> | |
406 Sign up | |
407 </a> </div> | |
408 </div> | |
409 </div> | |
410 </header> | |
411 | |
412 </div> | |
413 | |
414 <div id="start-of-content" class="show-on-focus"></div> | |
415 | |
416 | |
417 <div id="js-flash-container"> | |
418 | |
419 </div> | |
420 | |
421 | |
422 | |
423 <div class="application-main " data-commit-hovercards-enabled> | |
424 <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> | |
425 <main > | |
426 | |
427 | |
428 | |
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430 | |
431 | |
432 | |
433 | |
434 | |
435 | |
436 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav pt-0 pt-lg-4 "> | |
437 <div class="repohead-details-container clearfix container-lg p-responsive d-none d-lg-block"> | |
438 | |
439 <ul class="pagehead-actions"> | |
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448 Watch | |
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459 Star | |
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461 <a class="social-count js-social-count" href="/johnheap/VAPPER-Galaxy/stargazers" | |
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484 --><strong itemprop="name"><a data-pjax="#js-repo-pjax-container" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a></strong> | |
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713 | |
714 | |
715 | |
716 <div itemprop="text" class="Box-body p-0 blob-wrapper data type-python "> | |
717 | |
718 <table class="highlight tab-size js-file-line-container" data-tab-size="8"> | |
719 <tr> | |
720 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> | |
721 <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds">"""</span></span></td> | |
722 </tr> | |
723 <tr> | |
724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> | |
725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td> | |
726 </tr> | |
727 <tr> | |
728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> | |
729 <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> | |
730 </tr> | |
731 <tr> | |
732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> | |
733 <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> | |
734 </tr> | |
735 <tr> | |
736 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> | |
737 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> | |
738 </tr> | |
739 <tr> | |
740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> | |
741 <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> | |
742 </tr> | |
743 <tr> | |
744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> | |
745 <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> | |
746 </tr> | |
747 <tr> | |
748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> | |
749 <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> | |
750 </tr> | |
751 <tr> | |
752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> | |
753 <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> | |
754 </tr> | |
755 <tr> | |
756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> | |
757 <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> | |
758 </tr> | |
759 <tr> | |
760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> | |
761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> | |
762 </tr> | |
763 <tr> | |
764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> | |
765 <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> | |
766 </tr> | |
767 <tr> | |
768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> | |
769 <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> | |
770 </tr> | |
771 <tr> | |
772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> | |
773 <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> | |
774 </tr> | |
775 <tr> | |
776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> | |
777 <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> | |
778 </tr> | |
779 <tr> | |
780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> | |
781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td> | |
782 </tr> | |
783 <tr> | |
784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> | |
785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> | |
786 </tr> | |
787 <tr> | |
788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> | |
789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td> | |
790 </tr> | |
791 <tr> | |
792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> | |
793 <td id="LC19" class="blob-code blob-code-inner js-file-line"> | |
794 </td> | |
795 </tr> | |
796 <tr> | |
797 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> | |
798 <td id="LC20" class="blob-code blob-code-inner js-file-line"> | |
799 </td> | |
800 </tr> | |
801 <tr> | |
802 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> | |
803 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td> | |
804 </tr> | |
805 <tr> | |
806 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> | |
807 <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> | |
808 </tr> | |
809 <tr> | |
810 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> | |
811 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td> | |
812 </tr> | |
813 <tr> | |
814 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> | |
815 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td> | |
816 </tr> | |
817 <tr> | |
818 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> | |
819 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td> | |
820 </tr> | |
821 <tr> | |
822 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> | |
823 <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> | |
824 </tr> | |
825 <tr> | |
826 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> | |
827 <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> | |
828 </tr> | |
829 <tr> | |
830 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> | |
831 <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> | |
832 </tr> | |
833 <tr> | |
834 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> | |
835 <td id="LC29" class="blob-code blob-code-inner js-file-line"> | |
836 </td> | |
837 </tr> | |
838 <tr> | |
839 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> | |
840 <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> | |
841 </tr> | |
842 <tr> | |
843 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> | |
844 <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> | |
845 </tr> | |
846 <tr> | |
847 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> | |
848 <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> | |
849 </tr> | |
850 <tr> | |
851 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> | |
852 <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> | |
853 </tr> | |
854 <tr> | |
855 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> | |
856 <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> | |
857 </tr> | |
858 <tr> | |
859 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> | |
860 <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> | |
861 </tr> | |
862 <tr> | |
863 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> | |
864 <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> | |
865 </tr> | |
866 <tr> | |
867 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> | |
868 <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> | |
869 </tr> | |
870 <tr> | |
871 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> | |
872 <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> | |
873 </tr> | |
874 <tr> | |
875 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> | |
876 <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> | |
877 </tr> | |
878 <tr> | |
879 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> | |
880 <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> | |
881 </tr> | |
882 <tr> | |
883 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> | |
884 <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> | |
885 </tr> | |
886 <tr> | |
887 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> | |
888 <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> | |
889 </tr> | |
890 <tr> | |
891 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> | |
892 <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> | |
893 </tr> | |
894 <tr> | |
895 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> | |
896 <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> | |
897 </tr> | |
898 <tr> | |
899 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> | |
900 <td id="LC45" class="blob-code blob-code-inner js-file-line"> | |
901 </td> | |
902 </tr> | |
903 <tr> | |
904 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> | |
905 <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> | |
906 </tr> | |
907 <tr> | |
908 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> | |
909 <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> | |
910 </tr> | |
911 <tr> | |
912 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> | |
913 <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> | |
914 </tr> | |
915 <tr> | |
916 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> | |
917 <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> | |
918 </tr> | |
919 <tr> | |
920 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> | |
921 <td id="LC50" class="blob-code blob-code-inner js-file-line"> | |
922 </td> | |
923 </tr> | |
924 <tr> | |
925 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> | |
926 <td id="LC51" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td> | |
927 </tr> | |
928 <tr> | |
929 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> | |
930 <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> | |
931 </tr> | |
932 <tr> | |
933 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> | |
934 <td id="LC53" class="blob-code blob-code-inner js-file-line"> | |
935 </td> | |
936 </tr> | |
937 <tr> | |
938 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> | |
939 <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> | |
940 </tr> | |
941 <tr> | |
942 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> | |
943 <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> | |
944 </tr> | |
945 <tr> | |
946 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> | |
947 <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> | |
948 </tr> | |
949 <tr> | |
950 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> | |
951 <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> | |
952 </tr> | |
953 <tr> | |
954 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> | |
955 <td id="LC58" class="blob-code blob-code-inner js-file-line"> | |
956 </td> | |
957 </tr> | |
958 <tr> | |
959 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> | |
960 <td id="LC59" class="blob-code blob-code-inner js-file-line"> | |
961 </td> | |
962 </tr> | |
963 <tr> | |
964 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> | |
965 <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> | |
966 </tr> | |
967 <tr> | |
968 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> | |
969 <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> | |
970 </tr> | |
971 <tr> | |
972 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> | |
973 <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> | |
974 </tr> | |
975 <tr> | |
976 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> | |
977 <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> | |
978 </tr> | |
979 <tr> | |
980 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> | |
981 <td id="LC64" class="blob-code blob-code-inner js-file-line"> | |
982 </td> | |
983 </tr> | |
984 <tr> | |
985 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> | |
986 <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> | |
987 </tr> | |
988 <tr> | |
989 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> | |
990 <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> | |
991 </tr> | |
992 <tr> | |
993 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> | |
994 <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> | |
995 </tr> | |
996 <tr> | |
997 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> | |
998 <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> | |
999 </tr> | |
1000 <tr> | |
1001 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> | |
1002 <td id="LC69" class="blob-code blob-code-inner js-file-line"> | |
1003 </td> | |
1004 </tr> | |
1005 <tr> | |
1006 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> | |
1007 <td id="LC70" class="blob-code blob-code-inner js-file-line"> | |
1008 </td> | |
1009 </tr> | |
1010 <tr> | |
1011 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> | |
1012 <td id="LC71" class="blob-code blob-code-inner js-file-line"> | |
1013 </td> | |
1014 </tr> | |
1015 <tr> | |
1016 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> | |
1017 <td id="LC72" class="blob-code blob-code-inner js-file-line"> | |
1018 </td> | |
1019 </tr> | |
1020 <tr> | |
1021 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> | |
1022 <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> | |
1023 </tr> | |
1024 <tr> | |
1025 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> | |
1026 <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> | |
1027 </tr> | |
1028 <tr> | |
1029 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> | |
1030 <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> | |
1031 </tr> | |
1032 <tr> | |
1033 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> | |
1034 <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> | |
1035 </tr> | |
1036 <tr> | |
1037 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> | |
1038 <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> | |
1039 </tr> | |
1040 <tr> | |
1041 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> | |
1042 <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> | |
1043 </tr> | |
1044 <tr> | |
1045 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> | |
1046 <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> | |
1047 </tr> | |
1048 <tr> | |
1049 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> | |
1050 <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> | |
1051 </tr> | |
1052 <tr> | |
1053 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> | |
1054 <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> | |
1055 </tr> | |
1056 <tr> | |
1057 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> | |
1058 <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> | |
1059 </tr> | |
1060 <tr> | |
1061 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> | |
1062 <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> | |
1063 </tr> | |
1064 <tr> | |
1065 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> | |
1066 <td id="LC84" class="blob-code blob-code-inner js-file-line"> | |
1067 </td> | |
1068 </tr> | |
1069 <tr> | |
1070 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> | |
1071 <td id="LC85" class="blob-code blob-code-inner js-file-line"> | |
1072 </td> | |
1073 </tr> | |
1074 <tr> | |
1075 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> | |
1076 <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> | |
1077 </tr> | |
1078 <tr> | |
1079 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> | |
1080 <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> | |
1081 </tr> | |
1082 <tr> | |
1083 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> | |
1084 <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> | |
1085 </tr> | |
1086 <tr> | |
1087 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> | |
1088 <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> | |
1089 </tr> | |
1090 <tr> | |
1091 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> | |
1092 <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> | |
1093 </tr> | |
1094 <tr> | |
1095 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> | |
1096 <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> | |
1097 </tr> | |
1098 <tr> | |
1099 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> | |
1100 <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> | |
1101 </tr> | |
1102 <tr> | |
1103 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td> | |
1104 <td id="LC93" class="blob-code blob-code-inner js-file-line"> | |
1105 </td> | |
1106 </tr> | |
1107 <tr> | |
1108 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> | |
1109 <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> | |
1110 </tr> | |
1111 <tr> | |
1112 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td> | |
1113 <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> | |
1114 </tr> | |
1115 <tr> | |
1116 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> | |
1117 <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> | |
1118 </tr> | |
1119 <tr> | |
1120 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> | |
1121 <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> | |
1122 </tr> | |
1123 <tr> | |
1124 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> | |
1125 <td id="LC98" class="blob-code blob-code-inner js-file-line"> | |
1126 </td> | |
1127 </tr> | |
1128 <tr> | |
1129 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> | |
1130 <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> | |
1131 </tr> | |
1132 <tr> | |
1133 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> | |
1134 <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> | |
1135 </tr> | |
1136 <tr> | |
1137 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> | |
1138 <td id="LC101" class="blob-code blob-code-inner js-file-line"> | |
1139 </td> | |
1140 </tr> | |
1141 <tr> | |
1142 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> | |
1143 <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> | |
1144 </tr> | |
1145 <tr> | |
1146 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> | |
1147 <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> | |
1148 </tr> | |
1149 <tr> | |
1150 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> | |
1151 <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> | |
1152 </tr> | |
1153 <tr> | |
1154 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> | |
1155 <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> | |
1156 </tr> | |
1157 <tr> | |
1158 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> | |
1159 <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> | |
1160 </tr> | |
1161 <tr> | |
1162 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> | |
1163 <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> | |
1164 </tr> | |
1165 <tr> | |
1166 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> | |
1167 <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> | |
1168 </tr> | |
1169 <tr> | |
1170 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> | |
1171 <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> | |
1172 </tr> | |
1173 <tr> | |
1174 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> | |
1175 <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> | |
1176 </tr> | |
1177 <tr> | |
1178 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> | |
1179 <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> | |
1180 </tr> | |
1181 <tr> | |
1182 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> | |
1183 <td id="LC112" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td> | |
1184 </tr> | |
1185 <tr> | |
1186 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> | |
1187 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">while</span> line:</td> | |
1188 </tr> | |
1189 <tr> | |
1190 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> | |
1191 <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> | |
1192 </tr> | |
1193 <tr> | |
1194 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> | |
1195 <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> | |
1196 </tr> | |
1197 <tr> | |
1198 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> | |
1199 <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> | |
1200 </tr> | |
1201 <tr> | |
1202 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> | |
1203 <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> | |
1204 </tr> | |
1205 <tr> | |
1206 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> | |
1207 <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> | |
1208 </tr> | |
1209 <tr> | |
1210 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> | |
1211 <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> | |
1212 </tr> | |
1213 <tr> | |
1214 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td> | |
1215 <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> | |
1216 </tr> | |
1217 <tr> | |
1218 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> | |
1219 <td id="LC121" class="blob-code blob-code-inner js-file-line"> outfile.write(line)</td> | |
1220 </tr> | |
1221 <tr> | |
1222 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> | |
1223 <td id="LC122" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td> | |
1224 </tr> | |
1225 <tr> | |
1226 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> | |
1227 <td id="LC123" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line:</td> | |
1228 </tr> | |
1229 <tr> | |
1230 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> | |
1231 <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> | |
1232 </tr> | |
1233 <tr> | |
1234 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> | |
1235 <td id="LC125" class="blob-code blob-code-inner js-file-line"> outfile.write(line)</td> | |
1236 </tr> | |
1237 <tr> | |
1238 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> | |
1239 <td id="LC126" class="blob-code blob-code-inner js-file-line"> line<span class="pl-k">=</span>ref.readline()</td> | |
1240 </tr> | |
1241 <tr> | |
1242 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> | |
1243 <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> | |
1244 </tr> | |
1245 <tr> | |
1246 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> | |
1247 <td id="LC128" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span><span class="pl-bu">;</span></td> | |
1248 </tr> | |
1249 <tr> | |
1250 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> | |
1251 <td id="LC129" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> | |
1252 </tr> | |
1253 <tr> | |
1254 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> | |
1255 <td id="LC130" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td> | |
1256 </tr> | |
1257 <tr> | |
1258 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> | |
1259 <td id="LC131" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> | |
1260 </tr> | |
1261 <tr> | |
1262 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> | |
1263 <td id="LC132" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span>ref.readline()</td> | |
1264 </tr> | |
1265 <tr> | |
1266 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> | |
1267 <td id="LC133" class="blob-code blob-code-inner js-file-line"> ref.close()</td> | |
1268 </tr> | |
1269 <tr> | |
1270 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> | |
1271 <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> | |
1272 </tr> | |
1273 <tr> | |
1274 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> | |
1275 <td id="LC135" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> cuff_df</td> | |
1276 </tr> | |
1277 <tr> | |
1278 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> | |
1279 <td id="LC136" class="blob-code blob-code-inner js-file-line"> | |
1280 </td> | |
1281 </tr> | |
1282 <tr> | |
1283 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> | |
1284 <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> | |
1285 </tr> | |
1286 <tr> | |
1287 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> | |
1288 <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> | |
1289 </tr> | |
1290 <tr> | |
1291 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> | |
1292 <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> | |
1293 </tr> | |
1294 <tr> | |
1295 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> | |
1296 <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> | |
1297 </tr> | |
1298 <tr> | |
1299 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> | |
1300 <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> | |
1301 </tr> | |
1302 <tr> | |
1303 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> | |
1304 <td id="LC142" class="blob-code blob-code-inner js-file-line"> lineCounts <span class="pl-k">=</span> []</td> | |
1305 </tr> | |
1306 <tr> | |
1307 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td> | |
1308 <td id="LC143" class="blob-code blob-code-inner js-file-line"> compoundList <span class="pl-k">=</span> []</td> | |
1309 </tr> | |
1310 <tr> | |
1311 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td> | |
1312 <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> | |
1313 </tr> | |
1314 <tr> | |
1315 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td> | |
1316 <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> | |
1317 </tr> | |
1318 <tr> | |
1319 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td> | |
1320 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> | |
1321 </tr> | |
1322 <tr> | |
1323 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td> | |
1324 <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> | |
1325 </tr> | |
1326 <tr> | |
1327 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td> | |
1328 <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> | |
1329 </tr> | |
1330 <tr> | |
1331 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td> | |
1332 <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> | |
1333 </tr> | |
1334 <tr> | |
1335 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td> | |
1336 <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> | |
1337 </tr> | |
1338 <tr> | |
1339 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td> | |
1340 <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> | |
1341 </tr> | |
1342 <tr> | |
1343 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td> | |
1344 <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> | |
1345 </tr> | |
1346 <tr> | |
1347 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td> | |
1348 <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> | |
1349 </tr> | |
1350 <tr> | |
1351 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td> | |
1352 <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> | |
1353 </tr> | |
1354 <tr> | |
1355 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td> | |
1356 <td id="LC155" class="blob-code blob-code-inner js-file-line"> outList <span class="pl-k">=</span> []</td> | |
1357 </tr> | |
1358 <tr> | |
1359 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td> | |
1360 <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> | |
1361 </tr> | |
1362 <tr> | |
1363 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td> | |
1364 <td id="LC157" class="blob-code blob-code-inner js-file-line"> m <span class="pl-k">=</span> re.search(regex, line)</td> | |
1365 </tr> | |
1366 <tr> | |
1367 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td> | |
1368 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> m:</td> | |
1369 </tr> | |
1370 <tr> | |
1371 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td> | |
1372 <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> | |
1373 </tr> | |
1374 <tr> | |
1375 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td> | |
1376 <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> | |
1377 </tr> | |
1378 <tr> | |
1379 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td> | |
1380 <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> | |
1381 </tr> | |
1382 <tr> | |
1383 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td> | |
1384 <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> | |
1385 </tr> | |
1386 <tr> | |
1387 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td> | |
1388 <td id="LC163" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span></td> | |
1389 </tr> | |
1390 <tr> | |
1391 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td> | |
1392 <td id="LC164" class="blob-code blob-code-inner js-file-line"> compoundList.append(outList)</td> | |
1393 </tr> | |
1394 <tr> | |
1395 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td> | |
1396 <td id="LC165" class="blob-code blob-code-inner js-file-line"> lineCounts.append(n)</td> | |
1397 </tr> | |
1398 <tr> | |
1399 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td> | |
1400 <td id="LC166" class="blob-code blob-code-inner js-file-line"> hmmResult.close()</td> | |
1401 </tr> | |
1402 <tr> | |
1403 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td> | |
1404 <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> | |
1405 </tr> | |
1406 <tr> | |
1407 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td> | |
1408 <td id="LC168" class="blob-code blob-code-inner js-file-line"> | |
1409 </td> | |
1410 </tr> | |
1411 <tr> | |
1412 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td> | |
1413 <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> | |
1414 </tr> | |
1415 <tr> | |
1416 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td> | |
1417 <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> | |
1418 </tr> | |
1419 <tr> | |
1420 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td> | |
1421 <td id="LC171" class="blob-code blob-code-inner js-file-line"> countList <span class="pl-k">=</span> []</td> | |
1422 </tr> | |
1423 <tr> | |
1424 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td> | |
1425 <td id="LC172" class="blob-code blob-code-inner js-file-line"> weightList <span class="pl-k">=</span> []</td> | |
1426 </tr> | |
1427 <tr> | |
1428 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td> | |
1429 <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> | |
1430 </tr> | |
1431 <tr> | |
1432 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td> | |
1433 <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> | |
1434 </tr> | |
1435 <tr> | |
1436 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td> | |
1437 <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> | |
1438 </tr> | |
1439 <tr> | |
1440 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td> | |
1441 <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> | |
1442 </tr> | |
1443 <tr> | |
1444 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td> | |
1445 <td id="LC177" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> []</td> | |
1446 </tr> | |
1447 <tr> | |
1448 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td> | |
1449 <td id="LC178" class="blob-code blob-code-inner js-file-line"> weight <span class="pl-k">=</span> []</td> | |
1450 </tr> | |
1451 <tr> | |
1452 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td> | |
1453 <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> | |
1454 </tr> | |
1455 <tr> | |
1456 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td> | |
1457 <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> | |
1458 </tr> | |
1459 <tr> | |
1460 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td> | |
1461 <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> | |
1462 </tr> | |
1463 <tr> | |
1464 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td> | |
1465 <td id="LC182" class="blob-code blob-code-inner js-file-line"> countList.append(<span class="pl-c1">len</span>(t))</td> | |
1466 </tr> | |
1467 <tr> | |
1468 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td> | |
1469 <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> | |
1470 </tr> | |
1471 <tr> | |
1472 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td> | |
1473 <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> | |
1474 </tr> | |
1475 <tr> | |
1476 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td> | |
1477 <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> | |
1478 </tr> | |
1479 <tr> | |
1480 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td> | |
1481 <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> | |
1482 </tr> | |
1483 <tr> | |
1484 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td> | |
1485 <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> | |
1486 </tr> | |
1487 <tr> | |
1488 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td> | |
1489 <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> | |
1490 </tr> | |
1491 <tr> | |
1492 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td> | |
1493 <td id="LC189" class="blob-code blob-code-inner js-file-line"> weightList.append(wa)</td> | |
1494 </tr> | |
1495 <tr> | |
1496 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td> | |
1497 <td id="LC190" class="blob-code blob-code-inner js-file-line"> totalWeigth<span class="pl-k">+=</span>wa</td> | |
1498 </tr> | |
1499 <tr> | |
1500 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td> | |
1501 <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> | |
1502 </tr> | |
1503 <tr> | |
1504 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td> | |
1505 <td id="LC192" class="blob-code blob-code-inner js-file-line"> countList.append(totalCount)</td> | |
1506 </tr> | |
1507 <tr> | |
1508 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td> | |
1509 <td id="LC193" class="blob-code blob-code-inner js-file-line"> weightList.append(totalWeigth)</td> | |
1510 </tr> | |
1511 <tr> | |
1512 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td> | |
1513 <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> | |
1514 </tr> | |
1515 <tr> | |
1516 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td> | |
1517 <td id="LC195" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("--------")</span></td> | |
1518 </tr> | |
1519 <tr> | |
1520 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td> | |
1521 <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> | |
1522 </tr> | |
1523 <tr> | |
1524 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td> | |
1525 <td id="LC197" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print("--------")</span></td> | |
1526 </tr> | |
1527 <tr> | |
1528 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td> | |
1529 <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> countList,weightList</td> | |
1530 </tr> | |
1531 <tr> | |
1532 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td> | |
1533 <td id="LC199" class="blob-code blob-code-inner js-file-line"> | |
1534 </td> | |
1535 </tr> | |
1536 <tr> | |
1537 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td> | |
1538 <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> | |
1539 </tr> | |
1540 <tr> | |
1541 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td> | |
1542 <td id="LC201" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td> | |
1543 </tr> | |
1544 <tr> | |
1545 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td> | |
1546 <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> | |
1547 </tr> | |
1548 <tr> | |
1549 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td> | |
1550 <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> | |
1551 </tr> | |
1552 <tr> | |
1553 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td> | |
1554 <td id="LC204" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td> | |
1555 </tr> | |
1556 <tr> | |
1557 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td> | |
1558 <td id="LC205" class="blob-code blob-code-inner js-file-line"> | |
1559 </td> | |
1560 </tr> | |
1561 <tr> | |
1562 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td> | |
1563 <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> | |
1564 </tr> | |
1565 <tr> | |
1566 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td> | |
1567 <td id="LC207" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td> | |
1568 </tr> | |
1569 <tr> | |
1570 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td> | |
1571 <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> | |
1572 </tr> | |
1573 <tr> | |
1574 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td> | |
1575 <td id="LC209" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td> | |
1576 </tr> | |
1577 <tr> | |
1578 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td> | |
1579 <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> | |
1580 </tr> | |
1581 <tr> | |
1582 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td> | |
1583 <td id="LC211" class="blob-code blob-code-inner js-file-line"> | |
1584 </td> | |
1585 </tr> | |
1586 <tr> | |
1587 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td> | |
1588 <td id="LC212" class="blob-code blob-code-inner js-file-line"> | |
1589 </td> | |
1590 </tr> | |
1591 <tr> | |
1592 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td> | |
1593 <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> | |
1594 </tr> | |
1595 <tr> | |
1596 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td> | |
1597 <td id="LC214" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td> | |
1598 </tr> | |
1599 <tr> | |
1600 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td> | |
1601 <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> | |
1602 </tr> | |
1603 <tr> | |
1604 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td> | |
1605 <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> | |
1606 </tr> | |
1607 <tr> | |
1608 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td> | |
1609 <td id="LC217" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td> | |
1610 </tr> | |
1611 <tr> | |
1612 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td> | |
1613 <td id="LC218" class="blob-code blob-code-inner js-file-line"> | |
1614 </td> | |
1615 </tr> | |
1616 <tr> | |
1617 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td> | |
1618 <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> | |
1619 </tr> | |
1620 <tr> | |
1621 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td> | |
1622 <td id="LC220" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td> | |
1623 </tr> | |
1624 <tr> | |
1625 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td> | |
1626 <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> | |
1627 </tr> | |
1628 <tr> | |
1629 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td> | |
1630 <td id="LC222" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td> | |
1631 </tr> | |
1632 <tr> | |
1633 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td> | |
1634 <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> | |
1635 </tr> | |
1636 <tr> | |
1637 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td> | |
1638 <td id="LC224" class="blob-code blob-code-inner js-file-line"> | |
1639 </td> | |
1640 </tr> | |
1641 <tr> | |
1642 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td> | |
1643 <td id="LC225" class="blob-code blob-code-inner js-file-line"> | |
1644 </td> | |
1645 </tr> | |
1646 <tr> | |
1647 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td> | |
1648 <td id="LC226" class="blob-code blob-code-inner js-file-line"> | |
1649 </td> | |
1650 </tr> | |
1651 <tr> | |
1652 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td> | |
1653 <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> | |
1654 </tr> | |
1655 <tr> | |
1656 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td> | |
1657 <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> | |
1658 </tr> | |
1659 <tr> | |
1660 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td> | |
1661 <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> | |
1662 </tr> | |
1663 <tr> | |
1664 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td> | |
1665 <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> | |
1666 </tr> | |
1667 <tr> | |
1668 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td> | |
1669 <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> | |
1670 </tr> | |
1671 <tr> | |
1672 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td> | |
1673 <td id="LC232" class="blob-code blob-code-inner js-file-line"> | |
1674 </td> | |
1675 </tr> | |
1676 <tr> | |
1677 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td> | |
1678 <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> | |
1679 </tr> | |
1680 <tr> | |
1681 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td> | |
1682 <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> | |
1683 </tr> | |
1684 <tr> | |
1685 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td> | |
1686 <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> | |
1687 </tr> | |
1688 <tr> | |
1689 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td> | |
1690 <td id="LC236" class="blob-code blob-code-inner js-file-line"> | |
1691 </td> | |
1692 </tr> | |
1693 <tr> | |
1694 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td> | |
1695 <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> | |
1696 </tr> | |
1697 <tr> | |
1698 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td> | |
1699 <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> | |
1700 </tr> | |
1701 <tr> | |
1702 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td> | |
1703 <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> | |
1704 </tr> | |
1705 <tr> | |
1706 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td> | |
1707 <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> | |
1708 </tr> | |
1709 <tr> | |
1710 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td> | |
1711 <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> | |
1712 </tr> | |
1713 <tr> | |
1714 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td> | |
1715 <td id="LC242" class="blob-code blob-code-inner js-file-line"> | |
1716 </td> | |
1717 </tr> | |
1718 <tr> | |
1719 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td> | |
1720 <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> | |
1721 </tr> | |
1722 <tr> | |
1723 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td> | |
1724 <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> | |
1725 </tr> | |
1726 <tr> | |
1727 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td> | |
1728 <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> | |
1729 </tr> | |
1730 <tr> | |
1731 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td> | |
1732 <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> | |
1733 </tr> | |
1734 <tr> | |
1735 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td> | |
1736 <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> | |
1737 </tr> | |
1738 <tr> | |
1739 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td> | |
1740 <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> | |
1741 </tr> | |
1742 <tr> | |
1743 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td> | |
1744 <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> | |
1745 </tr> | |
1746 <tr> | |
1747 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td> | |
1748 <td id="LC250" class="blob-code blob-code-inner js-file-line"> plots <span class="pl-k">=</span> []</td> | |
1749 </tr> | |
1750 <tr> | |
1751 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td> | |
1752 <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> | |
1753 </tr> | |
1754 <tr> | |
1755 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td> | |
1756 <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> | |
1757 </tr> | |
1758 <tr> | |
1759 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td> | |
1760 <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> | |
1761 </tr> | |
1762 <tr> | |
1763 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td> | |
1764 <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> | |
1765 </tr> | |
1766 <tr> | |
1767 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td> | |
1768 <td id="LC255" class="blob-code blob-code-inner js-file-line"> fpos <span class="pl-k">+=</span>freqList[p]</td> | |
1769 </tr> | |
1770 <tr> | |
1771 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td> | |
1772 <td id="LC256" class="blob-code blob-code-inner js-file-line"> | |
1773 </td> | |
1774 </tr> | |
1775 <tr> | |
1776 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td> | |
1777 <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> | |
1778 </tr> | |
1779 <tr> | |
1780 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td> | |
1781 <td id="LC258" class="blob-code blob-code-inner js-file-line"> vpos <span class="pl-k">+=</span>VAPtable[p]</td> | |
1782 </tr> | |
1783 <tr> | |
1784 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td> | |
1785 <td id="LC259" class="blob-code blob-code-inner js-file-line"> | |
1786 </td> | |
1787 </tr> | |
1788 <tr> | |
1789 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td> | |
1790 <td id="LC260" class="blob-code blob-code-inner js-file-line"> plots.append(tp)</td> | |
1791 </tr> | |
1792 <tr> | |
1793 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td> | |
1794 <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> | |
1795 </tr> | |
1796 <tr> | |
1797 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td> | |
1798 <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> | |
1799 </tr> | |
1800 <tr> | |
1801 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td> | |
1802 <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> | |
1803 </tr> | |
1804 <tr> | |
1805 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td> | |
1806 <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> | |
1807 </tr> | |
1808 <tr> | |
1809 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td> | |
1810 <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> | |
1811 </tr> | |
1812 <tr> | |
1813 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td> | |
1814 <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> | |
1815 </tr> | |
1816 <tr> | |
1817 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td> | |
1818 <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> | |
1819 </tr> | |
1820 <tr> | |
1821 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td> | |
1822 <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> | |
1823 </tr> | |
1824 <tr> | |
1825 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td> | |
1826 <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> | |
1827 </tr> | |
1828 <tr> | |
1829 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td> | |
1830 <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> | |
1831 </tr> | |
1832 <tr> | |
1833 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td> | |
1834 <td id="LC271" class="blob-code blob-code-inner js-file-line"> | |
1835 </td> | |
1836 </tr> | |
1837 <tr> | |
1838 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td> | |
1839 <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> | |
1840 </tr> | |
1841 <tr> | |
1842 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td> | |
1843 <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> | |
1844 </tr> | |
1845 <tr> | |
1846 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td> | |
1847 <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> | |
1848 </tr> | |
1849 <tr> | |
1850 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td> | |
1851 <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> | |
1852 </tr> | |
1853 <tr> | |
1854 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td> | |
1855 <td id="LC276" class="blob-code blob-code-inner js-file-line"> | |
1856 </td> | |
1857 </tr> | |
1858 <tr> | |
1859 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td> | |
1860 <td id="LC277" class="blob-code blob-code-inner js-file-line"> | |
1861 </td> | |
1862 </tr> | |
1863 <tr> | |
1864 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td> | |
1865 <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> | |
1866 </tr> | |
1867 <tr> | |
1868 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td> | |
1869 <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> | |
1870 </tr> | |
1871 <tr> | |
1872 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td> | |
1873 <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> | |
1874 </tr> | |
1875 <tr> | |
1876 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td> | |
1877 <td id="LC281" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> name</td> | |
1878 </tr> | |
1879 <tr> | |
1880 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td> | |
1881 <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> | |
1882 </tr> | |
1883 <tr> | |
1884 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td> | |
1885 <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> | |
1886 </tr> | |
1887 <tr> | |
1888 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td> | |
1889 <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> | |
1890 </tr> | |
1891 <tr> | |
1892 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td> | |
1893 <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> | |
1894 </tr> | |
1895 <tr> | |
1896 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td> | |
1897 <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> | |
1898 </tr> | |
1899 <tr> | |
1900 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td> | |
1901 <td id="LC287" class="blob-code blob-code-inner js-file-line"> | |
1902 </td> | |
1903 </tr> | |
1904 <tr> | |
1905 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td> | |
1906 <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> | |
1907 </tr> | |
1908 <tr> | |
1909 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td> | |
1910 <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> | |
1911 </tr> | |
1912 <tr> | |
1913 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td> | |
1914 <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> | |
1915 </tr> | |
1916 <tr> | |
1917 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td> | |
1918 <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> | |
1919 </tr> | |
1920 <tr> | |
1921 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td> | |
1922 <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> | |
1923 </tr> | |
1924 <tr> | |
1925 <td id="L293" class="blob-num js-line-number" data-line-number="293"></td> | |
1926 <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> | |
1927 </tr> | |
1928 <tr> | |
1929 <td id="L294" class="blob-num js-line-number" data-line-number="294"></td> | |
1930 <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> | |
1931 </tr> | |
1932 <tr> | |
1933 <td id="L295" class="blob-num js-line-number" data-line-number="295"></td> | |
1934 <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> | |
1935 </tr> | |
1936 <tr> | |
1937 <td id="L296" class="blob-num js-line-number" data-line-number="296"></td> | |
1938 <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> | |
1939 </tr> | |
1940 <tr> | |
1941 <td id="L297" class="blob-num js-line-number" data-line-number="297"></td> | |
1942 <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> | |
1943 </tr> | |
1944 <tr> | |
1945 <td id="L298" class="blob-num js-line-number" data-line-number="298"></td> | |
1946 <td id="LC298" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> | |
1947 </tr> | |
1948 <tr> | |
1949 <td id="L299" class="blob-num js-line-number" data-line-number="299"></td> | |
1950 <td id="LC299" class="blob-code blob-code-inner js-file-line"> | |
1951 </td> | |
1952 </tr> | |
1953 <tr> | |
1954 <td id="L300" class="blob-num js-line-number" data-line-number="300"></td> | |
1955 <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> | |
1956 </tr> | |
1957 <tr> | |
1958 <td id="L301" class="blob-num js-line-number" data-line-number="301"></td> | |
1959 <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> | |
1960 </tr> | |
1961 <tr> | |
1962 <td id="L302" class="blob-num js-line-number" data-line-number="302"></td> | |
1963 <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> | |
1964 </tr> | |
1965 <tr> | |
1966 <td id="L303" class="blob-num js-line-number" data-line-number="303"></td> | |
1967 <td id="LC303" class="blob-code blob-code-inner js-file-line"> | |
1968 </td> | |
1969 </tr> | |
1970 <tr> | |
1971 <td id="L304" class="blob-num js-line-number" data-line-number="304"></td> | |
1972 <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> | |
1973 </tr> | |
1974 <tr> | |
1975 <td id="L305" class="blob-num js-line-number" data-line-number="305"></td> | |
1976 <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> | |
1977 </tr> | |
1978 <tr> | |
1979 <td id="L306" class="blob-num js-line-number" data-line-number="306"></td> | |
1980 <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> | |
1981 </tr> | |
1982 <tr> | |
1983 <td id="L307" class="blob-num js-line-number" data-line-number="307"></td> | |
1984 <td id="LC307" class="blob-code blob-code-inner js-file-line"> | |
1985 </td> | |
1986 </tr> | |
1987 <tr> | |
1988 <td id="L308" class="blob-num js-line-number" data-line-number="308"></td> | |
1989 <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> | |
1990 </tr> | |
1991 <tr> | |
1992 <td id="L309" class="blob-num js-line-number" data-line-number="309"></td> | |
1993 <td id="LC309" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> | |
1994 </tr> | |
1995 <tr> | |
1996 <td id="L310" class="blob-num js-line-number" data-line-number="310"></td> | |
1997 <td id="LC310" class="blob-code blob-code-inner js-file-line"> | |
1998 </td> | |
1999 </tr> | |
2000 <tr> | |
2001 <td id="L311" class="blob-num js-line-number" data-line-number="311"></td> | |
2002 <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> | |
2003 </tr> | |
2004 <tr> | |
2005 <td id="L312" class="blob-num js-line-number" data-line-number="312"></td> | |
2006 <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> | |
2007 </tr> | |
2008 <tr> | |
2009 <td id="L313" class="blob-num js-line-number" data-line-number="313"></td> | |
2010 <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> | |
2011 </tr> | |
2012 <tr> | |
2013 <td id="L314" class="blob-num js-line-number" data-line-number="314"></td> | |
2014 <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> | |
2015 </tr> | |
2016 <tr> | |
2017 <td id="L315" class="blob-num js-line-number" data-line-number="315"></td> | |
2018 <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> | |
2019 </tr> | |
2020 <tr> | |
2021 <td id="L316" class="blob-num js-line-number" data-line-number="316"></td> | |
2022 <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> | |
2023 </tr> | |
2024 <tr> | |
2025 <td id="L317" class="blob-num js-line-number" data-line-number="317"></td> | |
2026 <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> | |
2027 </tr> | |
2028 <tr> | |
2029 <td id="L318" class="blob-num js-line-number" data-line-number="318"></td> | |
2030 <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> | |
2031 </tr> | |
2032 <tr> | |
2033 <td id="L319" class="blob-num js-line-number" data-line-number="319"></td> | |
2034 <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> | |
2035 </tr> | |
2036 <tr> | |
2037 <td id="L320" class="blob-num js-line-number" data-line-number="320"></td> | |
2038 <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> | |
2039 </tr> | |
2040 <tr> | |
2041 <td id="L321" class="blob-num js-line-number" data-line-number="321"></td> | |
2042 <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> | |
2043 </tr> | |
2044 <tr> | |
2045 <td id="L322" class="blob-num js-line-number" data-line-number="322"></td> | |
2046 <td id="LC322" class="blob-code blob-code-inner js-file-line"> | |
2047 </td> | |
2048 </tr> | |
2049 <tr> | |
2050 <td id="L323" class="blob-num js-line-number" data-line-number="323"></td> | |
2051 <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> | |
2052 </tr> | |
2053 <tr> | |
2054 <td id="L324" class="blob-num js-line-number" data-line-number="324"></td> | |
2055 <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> | |
2056 </tr> | |
2057 <tr> | |
2058 <td id="L325" class="blob-num js-line-number" data-line-number="325"></td> | |
2059 <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> | |
2060 </tr> | |
2061 <tr> | |
2062 <td id="L326" class="blob-num js-line-number" data-line-number="326"></td> | |
2063 <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> | |
2064 </tr> | |
2065 <tr> | |
2066 <td id="L327" class="blob-num js-line-number" data-line-number="327"></td> | |
2067 <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> | |
2068 </tr> | |
2069 <tr> | |
2070 <td id="L328" class="blob-num js-line-number" data-line-number="328"></td> | |
2071 <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> | |
2072 </tr> | |
2073 <tr> | |
2074 <td id="L329" class="blob-num js-line-number" data-line-number="329"></td> | |
2075 <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> | |
2076 </tr> | |
2077 <tr> | |
2078 <td id="L330" class="blob-num js-line-number" data-line-number="330"></td> | |
2079 <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> | |
2080 </tr> | |
2081 <tr> | |
2082 <td id="L331" class="blob-num js-line-number" data-line-number="331"></td> | |
2083 <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> | |
2084 </tr> | |
2085 <tr> | |
2086 <td id="L332" class="blob-num js-line-number" data-line-number="332"></td> | |
2087 <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> | |
2088 </tr> | |
2089 <tr> | |
2090 <td id="L333" class="blob-num js-line-number" data-line-number="333"></td> | |
2091 <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> | |
2092 </tr> | |
2093 <tr> | |
2094 <td id="L334" class="blob-num js-line-number" data-line-number="334"></td> | |
2095 <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> | |
2096 </tr> | |
2097 <tr> | |
2098 <td id="L335" class="blob-num js-line-number" data-line-number="335"></td> | |
2099 <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> | |
2100 </tr> | |
2101 <tr> | |
2102 <td id="L336" class="blob-num js-line-number" data-line-number="336"></td> | |
2103 <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> | |
2104 </tr> | |
2105 <tr> | |
2106 <td id="L337" class="blob-num js-line-number" data-line-number="337"></td> | |
2107 <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> | |
2108 </tr> | |
2109 <tr> | |
2110 <td id="L338" class="blob-num js-line-number" data-line-number="338"></td> | |
2111 <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> | |
2112 </tr> | |
2113 <tr> | |
2114 <td id="L339" class="blob-num js-line-number" data-line-number="339"></td> | |
2115 <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> | |
2116 </tr> | |
2117 <tr> | |
2118 <td id="L340" class="blob-num js-line-number" data-line-number="340"></td> | |
2119 <td id="LC340" class="blob-code blob-code-inner js-file-line"> | |
2120 </td> | |
2121 </tr> | |
2122 <tr> | |
2123 <td id="L341" class="blob-num js-line-number" data-line-number="341"></td> | |
2124 <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> | |
2125 </tr> | |
2126 <tr> | |
2127 <td id="L342" class="blob-num js-line-number" data-line-number="342"></td> | |
2128 <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> | |
2129 </tr> | |
2130 <tr> | |
2131 <td id="L343" class="blob-num js-line-number" data-line-number="343"></td> | |
2132 <td id="LC343" class="blob-code blob-code-inner js-file-line"> | |
2133 </td> | |
2134 </tr> | |
2135 <tr> | |
2136 <td id="L344" class="blob-num js-line-number" data-line-number="344"></td> | |
2137 <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> | |
2138 </tr> | |
2139 <tr> | |
2140 <td id="L345" class="blob-num js-line-number" data-line-number="345"></td> | |
2141 <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> | |
2142 </tr> | |
2143 </table> | |
2144 | |
2145 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true"> | |
2146 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar"> | |
2147 <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> | |
2148 </summary> | |
2149 <details-menu> | |
2150 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px"> | |
2151 <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> | |
2152 <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> | |
2153 <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> | |
2154 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li> | |
2155 </ul> | |
2156 </details-menu> | |
2157 </details> | |
2158 | |
2159 </div> | |
2160 | |
2161 </div> | |
2162 | |
2163 | |
2164 | |
2165 <details class="details-reset details-overlay details-overlay-dark"> | |
2166 <summary data-hotkey="l" aria-label="Jump to line"></summary> | |
2167 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line"> | |
2168 <!-- '"` --><!-- </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="✓" /> | |
2169 <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> | |
2170 <button type="submit" class="btn" data-close-dialog>Go</button> | |
2171 </form> </details-dialog> | |
2172 </details> | |
2173 | |
2174 | |
2175 | |
2176 </div> | |
2177 <div class="modal-backdrop js-touch-events"></div> | |
2178 </div> | |
2179 | |
2180 </main> | |
2181 </div> | |
2182 | |
2183 | |
2184 </div> | |
2185 | |
2186 | |
2187 <div class="footer container-lg width-full p-responsive" role="contentinfo"> | |
2188 <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 "> | |
2189 <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"> | |
2190 <li class="mr-3 mr-lg-0">© 2019 <span title="0.38259s from unicorn-7478f9985c-skxnd">GitHub</span>, Inc.</li> | |
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2195 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li> | |
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2198 <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com"> | |
2199 <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> | |
2200 </a> | |
2201 <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"> | |
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2211 <div class="d-flex flex-justify-center pb-6"> | |
2212 <span class="f6 text-gray-light"></span> | |
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2214 </div> | |
2215 | |
2216 | |
2217 | |
2218 <div id="ajax-error-message" class="ajax-error-message flash flash-error"> | |
2219 <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> | |
2220 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> | |
2221 <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> | |
2222 </button> | |
2223 You can’t perform that action at this time. | |
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2225 | |
2226 | |
2227 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script> | |
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2230 <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script> | |
2231 | |
2232 | |
2233 | |
2234 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden | |
2235 > | |
2236 <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> | |
2237 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span> | |
2238 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span> | |
2239 </div> | |
2240 <template id="site-details-dialog"> | |
2241 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open> | |
2242 <summary role="button" aria-label="Close dialog"></summary> | |
2243 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal"> | |
2244 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog> | |
2245 <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> | |
2246 </button> | |
2247 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div> | |
2248 </details-dialog> | |
2249 </details> | |
2250 </template> | |
2251 | |
2252 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0"> | |
2253 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;"> | |
2254 </div> | |
2255 </div> | |
2256 | |
2257 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div> | |
2258 | |
2259 </body> | |
2260 </html> | |
2261 |