Mercurial > repos > johnheap > vapper
comparison Tryp_V.py @ 18:e7da2274c9f6 draft
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author | johnheap |
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date | Mon, 03 Jun 2019 16:00:24 -0400 |
parents | e75a85590041 |
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17:5e346d75ccf3 | 18:e7da2274c9f6 |
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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 import matplotlib as mpl |
21 <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" /> | 21 mpl.use('Agg') |
22 <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" /> | 22 |
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 subprocess |
24 | 24 import shutil |
25 | 25 import re |
26 | 26 import pandas as pd |
27 | 27 import os |
28 | 28 |
29 <meta name="viewport" content="width=device-width"> | 29 import sys |
30 | 30 |
31 <title>VAPPER-Galaxy/Tryp_V.py at master · johnheap/VAPPER-Galaxy · GitHub</title> | 31 import matplotlib.pyplot as plt |
32 <meta name="description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub."> | 32 from matplotlib.patches import Patch |
33 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> | 33 import seaborn as sns |
34 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> | 34 |
35 <meta property="fb:app_id" content="1401488693436528"> | 35 def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name): |
36 | 36 #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq" |
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 argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name |
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 print(argString) |
39 | 39 returncode = subprocess.call(argString, shell=True) |
40 <link rel="assets" href="https://github.githubassets.com/"> | 40 if returncode != 0: |
41 | 41 return "Error in velveth" |
42 <meta name="pjax-timeout" content="1000"> | 42 argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -clean yes -ins_length_sd 50 -min_pair_count 20" |
43 | 43 #argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20" |
44 <meta name="request-id" content="99EA:03C4:48319:89CA2:5CF56242" data-pjax-transient> | 44 #argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString |
45 | 45 print(argString) |
46 | 46 returncode = subprocess.call(argString, shell = True) |
47 | 47 if returncode != 0: |
48 | 48 return "Error in velvetg" |
49 <meta name="selected-link" value="repo_source" data-pjax-transient> | 49 shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa") # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa"; |
50 | 50 return "ok" |
51 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> | 51 |
52 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> | 52 |
53 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc"> | 53 def blastContigs(test_name,database): |
54 | 54 print(test_name) |
55 <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="99EA:03C4:48319:89CA2:5CF56242" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" /> | 55 print(database) |
56 <meta name="analytics-location" content="/<user-name>/<repo-name>/blob/show" data-pjax-transient="true" /> | 56 #db_path = os.path.dirname(os.path.realpath(__file__))+database |
57 | 57 db_path = database |
58 | 58 argString = "blastn -db "+db_path+" -query "+test_name+".fa -outfmt 10 -out "+test_name+"_blast.txt" |
59 | 59 print(argString) |
60 <meta name="google-analytics" content="UA-3769691-2"> | 60 returncode = subprocess.call(argString, shell = True) |
61 | 61 if returncode != 0: |
62 | 62 return "Error in blastall" |
63 <meta class="js-ga-set" name="dimension1" content="Logged Out"> | 63 blast_df = pd.read_csv(""+test_name+"_blast.txt") |
64 | 64 #print (blast_df) |
65 | 65 #if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){ |
66 | 66 #'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore' |
67 | 67 blast_df.columns = ['qaccver', 'saccver', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue','bitscore'] |
68 | 68 blastResult_df = blast_df[(blast_df['pident']>=98) & (blast_df['length'] > 100) & (blast_df['evalue']<0.001) ] |
69 <meta name="hostname" content="github.com"> | 69 blastResult_df = blastResult_df[['qaccver', 'saccver', 'pident']] #query accession.version, subject accession.version, Percentage of identical matches |
70 <meta name="user-login" content=""> | 70 |
71 | 71 return blastResult_df |
72 <meta name="expected-hostname" content="github.com"> | 72 |
73 <meta name="js-proxy-site-detection-payload" content="YzYyMzAwYTYwMTZlZjQ5YWUzNGIzNTY5ZmQ2NTkxYTVmNWQzYzA5NjdiMTY5MDUxNDBjODNkMjI2NjY2NDk3Znx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiI5OUVBOjAzQzQ6NDgzMTk6ODlDQTI6NUNGNTYyNDIiLCJ0aW1lc3RhbXAiOjE1NTk1ODUzNDYsImhvc3QiOiJnaXRodWIuY29tIn0="> | 73 |
74 | 74 |
75 <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS"> | 75 def getCogsPresent(blastResult_df,strain,cogOrBinList): |
76 | 76 blastResult_df.sort_values('pident',axis = 0, ascending=False, inplace=True) |
77 <meta name="html-safe-nonce" content="8f60f90a25489bbe59ea08995f73407524f71ec9"> | 77 nodeList = blastResult_df['qaccver'].tolist() |
78 | 78 cogList = blastResult_df['saccver'].tolist() |
79 <meta http-equiv="x-pjax-version" content="af1499c2254d0582d0a98af1dfd7f11b"> | 79 cogSet = set(cogList) #get unique values |
80 | 80 cogList = sorted(cogSet) #sort them |
81 | 81 |
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 #print (cogList) |
83 | 83 #print (len(cogList)) |
84 <meta name="go-import" content="github.com/johnheap/VAPPER-Galaxy git https://github.com/johnheap/VAPPER-Galaxy.git"> | 84 |
85 | 85 thereList = [] |
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 dataList = [] |
87 | 87 #dir_path = os.path.dirname(os.path.realpath(__file__)) |
88 | 88 fname = cogOrBinList |
89 <link rel="canonical" href="https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py" data-pjax-transient> | 89 cnt = 0 |
90 | 90 with open (fname) as f: |
91 | 91 for line in f: |
92 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats"> | 92 dataList.append(line.rstrip('\n\r ')) |
93 | 93 if line.rstrip('\n\r ') in cogList: |
94 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors"> | 94 thereList.append('1') |
95 | 95 cnt = cnt+1 |
96 <link rel="mask-icon" href="https://github.githubassets.com/pinned-octocat.svg" color="#000000"> | 96 else: |
97 <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://github.githubassets.com/favicon.ico"> | 97 thereList.append('0') |
98 | 98 |
99 <meta name="theme-color" content="#1e2327"> | 99 #print (thereList) |
100 | 100 #print (cnt) |
101 | 101 data = {'Cog': dataList, strain: thereList} |
102 | 102 presence_df = pd.DataFrame(data) |
103 | 103 #print (presence_df) |
104 | 104 return presence_df |
105 <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials"> | 105 |
106 | 106 def addToCurrentData(cog_df, name): |
107 </head> | 107 dir_path = os.path.dirname(os.path.realpath(__file__)) |
108 | 108 j_fname = dir_path + r"/data/vivax/TvDatabase.csv" |
109 <body class="logged-out env-production page-responsive page-blob"> | 109 tv_df = pd.read_csv(j_fname) |
110 | 110 |
111 | 111 cogList = cog_df[name].tolist() |
112 <div class="position-relative js-header-wrapper "> | 112 #cogList.insert(0,'Test') |
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 #print (len(tv_df)) |
114 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div> | 114 #print(len(cogList)) |
115 | 115 |
116 | 116 #print(cogList) |
117 | 117 tv_df.loc[:,name]=cogList |
118 | 118 return tv_df |
119 | 119 |
120 | 120 |
121 <header class="Header-old header-logged-out js-details-container Details position-relative f4 py-2" role="banner"> | 121 |
122 <div class="container-lg d-lg-flex flex-items-center p-responsive"> | 122 |
123 <div class="d-flex flex-justify-between flex-items-center"> | 123 def createClusterMap(tv_df,name,html_path,pdfExport): |
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 #Retrieve Data |
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 dir_path = os.path.dirname(os.path.realpath(__file__)) |
126 </a> | 126 j_fname = dir_path+r"/data/vivax/geoTv.csv" |
127 | 127 geo_df = pd.read_csv(j_fname) |
128 <div class="d-lg-none css-truncate css-truncate-target width-fit p-2"> | 128 geo_df.loc[len(geo_df)] =[name,name,'k'] |
129 | 129 print(geo_df) |
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 |
131 <a class="Header-link" href="/johnheap">johnheap</a> | 131 myStrains = tv_df.columns.values.tolist() #beware first entry is COG |
132 / | 132 myStrains = myStrains[1:] |
133 <a class="Header-link" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a> | 133 print(myStrains) |
134 | 134 myPal = [] |
135 | 135 for s in myStrains: |
136 </div> | 136 col = geo_df[(geo_df['Strain'] == s)]['colour'].tolist() |
137 | 137 myPal.append(col[0]) |
138 <div class="d-flex flex-items-center"> | 138 print(myPal) |
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":"99EA:03C4:48319:89CA2:5CF56242","originating_url":"https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py","referrer":null,"user_id":null}}" data-hydro-click-hmac="2b5b3e285e06f6291d9585d00d3c451a25d337d3be9971ebaefb9cb398fb4ecc" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo"> | 139 mycogmap = ['skyblue', 'orangered'] # blue absent,red present |
140 Sign up | 140 tv_df.set_index('COG', inplace=True) |
141 </a> | 141 tv_df = tv_df[tv_df.columns].astype(float) |
142 <button class="btn-link d-lg-none mt-1 js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false"> | 142 |
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 cg = sns.clustermap(tv_df, method='ward', col_colors=myPal, cmap=mycogmap, yticklabels = 1500, row_cluster=False, linewidths = 0) |
144 </button> | 144 #cg = sns.clustermap(tv_df, method='ward', row_cluster=False, linewidths = 0) |
145 </div> | 145 ax = cg.ax_heatmap |
146 </div> | 146 #xasix ticks and labels. |
147 | 147 ax.xaxis.tick_top() #set ticks at top |
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 newlabs = [] |
149 <div class="d-flex d-lg-none flex-justify-end border-bottom bg-gray-light p-3"> | 149 |
150 <button class="btn-link js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false"> | 150 labs = ax.xaxis.get_ticklabels() |
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 for i in range(0, len(labs)): |
152 </button> | 152 print(labs[i]) |
153 </div> | 153 # labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars |
154 | 154 newlabs.append(" " + labs[i].get_text()) |
155 <nav class="mt-0 px-3 px-lg-0 mb-5 mb-lg-0" aria-label="Global"> | 155 ax.xaxis.set_ticklabels(newlabs) |
156 <ul class="d-lg-flex list-style-none"> | 156 |
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 #labs = ax.xaxis.get_ticklabels() |
158 <details class="HeaderMenu-details details-overlay details-reset width-full"> | 158 #for i in range(0, len(labs)): |
159 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> | 159 # print(labs[i]) |
160 Why GitHub? | 160 # labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars |
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 # print(labs[i]) |
162 <path d="M1,1l6.2,6L13,1"></path> | 162 #ax.xaxis.set_ticklabels(labs) |
163 </svg> | 163 plt.setp(cg.ax_heatmap.xaxis.get_ticklabels(), rotation=90) # get x labels printed vertically |
164 </summary> | 164 |
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 cg.cax.set_visible(False) |
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 ax = cg.ax_heatmap |
167 <ul class="list-style-none f5 pb-3"> | 167 ax.set_yticklabels("") |
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 ax.set_ylabel("") |
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 ax = cg.ax_heatmap |
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 # ax.set_title("Variant antigen profiles of T. vivax genomes.\nDendrogram reflects the VSG repertoire relationships of each strain inferred by the presence and absence of non-universal T. vivax VSG orthologs.", va = "top", wrap = "True") |
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 b = len(tv_df) |
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 print(b) |
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 title = "Figure Legend: The Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ " \ |
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 "showing the \ncombination of present and absent diagnostic cluster of VSG orthologs " \ |
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 "across the sample cohort. \nDendrogram reflects the relationships amongst the VSG" \ |
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 " repertoires of each strain. " \ |
177 </ul> | 177 "Strains were isolated \nfrom multiple African countries as shown in the key.\nData was produced with the " \ |
178 | 178 "'Variant Antigen Profiler' (Silva Pereira et al., 2019)." |
179 <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> | 179 |
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 ax.text(-1.5, len(tv_df) + 8, |
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 title, |
182 </ul> | 182 ha="left", va="top", wrap="True") |
183 </div> | 183 col = cg.ax_col_dendrogram.get_position() |
184 </details> | 184 cg.ax_col_dendrogram.set_position([col.x0, col.y0*1.08, col.width, col.height*1.1]) |
185 </li> | 185 |
186 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> | 186 countryList = pd.unique(geo_df['Location']) |
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 colourList = pd.unique(geo_df['colour']) |
188 </li> | 188 legend_elements = [Patch(facecolor='orangered', label='COG Present'), |
189 | 189 Patch(facecolor='skyblue', label='COG Absent')] |
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 |
191 <details class="HeaderMenu-details details-overlay details-reset width-full"> | 191 for i in range(0, len(colourList)): |
192 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> | 192 print("country = %s, colour = %s" % (countryList[i], colourList[i])) |
193 Explore | 193 p = Patch(facecolor=str(colourList[i]), label=countryList[i]) |
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 legend_elements.append(p) |
195 <path d="M1,1l6.2,6L13,1"></path> | 195 |
196 </svg> | 196 ax.legend(handles = legend_elements, bbox_to_anchor=(-0.3,1.2),loc = 'upper left') |
197 </summary> | 197 |
198 | 198 |
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 |
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 |
202 </ul> | 202 |
203 | 203 |
204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn & contribute</h4> | 204 #plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0 ) # get y labels printed horizontally |
205 <ul class="list-style-none mb-3"> | 205 # cg.dendrogram_col.linkage # linkage matrix for columns |
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 # cg.dendrogram_row.linkage # linkage matrix for rows |
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 # plt.savefig(r"results/" + name + "_heatmap.png") |
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 #plt.savefig(htmlresource + "/heatmap.png") |
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 #if pdf == 'PDF_Yes': |
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 # plt.savefig(htmlresource + "/heatmap.pdf") |
211 </ul> | 211 # shutil.copyfile("heatmap.pdf",heatmapfn) # |
212 | 212 #plt.legend() |
213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4> | 213 fname = html_path+"/"+name+"_clustermap.png" |
214 <ul class="list-style-none mb-0"> | 214 cg.savefig(fname) |
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 if pdfExport == 'PDF_Yes': |
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 fname = html_path + "/" + name + "_clustermap.pdf" |
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 cg.savefig(fname) |
218 </ul> | 218 #plt.show() |
219 </div> | 219 |
220 </details> | 220 def createHTML(name,htmlfn,htmlPath): |
221 </li> | 221 #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource |
222 | 222 htmlString = r"<html><title>T.vivax VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3>" |
223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> | 223 htmlString += name |
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 htmlString += r'<p> <h3>The Heat Map and Dendrogram</h3></p>' |
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 imgString = r"<img src = '"+name+"_clustermap.png' alt='Cog Clustermap' style='max-width:100%'><br><br>" |
228 <details class="HeaderMenu-details details-overlay details-reset width-full"> | 228 htmlString += imgString |
229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> | 229 print(htmlString) |
230 Pricing | 230 |
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 with open(htmlfn, "w") as htmlfile: |
232 <path d="M1,1l6.2,6L13,1"></path> | 232 htmlfile.write(htmlString) |
233 </svg> | 233 |
234 </summary> | 234 |
235 | 235 def vivax_assemble(args,dict): |
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 #argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10} |
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 #assembleWithVelvet("V2_Test", '65', '400', '5', "data/TviBrRp.1.clean", "data/TviBrRp.2.clean") |
238 | 238 |
239 <ul class="list-style-none mb-3"> | 239 vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax" |
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 assembleWithVelvet(args[dict['name']], args[dict['kmers']], args[dict['inslen']], args[dict['covcut']], |
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 args[dict['forward']], args[dict['reverse']]) |
242 </ul> | 242 blastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/COGs.fas") |
243 | 243 orthPresence_df = getCogsPresent(blastResult_df, args[dict['name']], vivaxPath+r"/Database/COGlist.txt") |
244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> | 244 |
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 binBlastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/Bin_2.fas") |
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 binPresence_df = getCogsPresent(binBlastResult_df, args[dict['name']], vivaxPath+r"/Database/binlist.txt") |
247 </ul> | 247 cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True) |
248 </div> | 248 |
249 </details> | 249 fname = args[dict['html_resource']] +args[dict['name']]+"_cogspresent.csv" |
250 </li> | 250 cogPresence_df.to_csv(fname) |
251 </ul> | 251 current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. |
252 </nav> | 252 createClusterMap(current_df, args[dict['name']],args[dict['html_resource']],args[dict['pdfexport']]) |
253 | 253 createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']]) |
254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left"> | 254 |
255 <div class="d-lg-flex mb-3 mb-lg-0"> | 255 def test_cluster(args,dict): |
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 print ("name: %s",args[dict['name']]) |
257 role="combobox" | 257 cogPresence_df = pd.read_csv("test_cogspresent.csv") |
258 aria-owns="jump-to-results" | 258 print(cogPresence_df) |
259 aria-label="Search or jump to" | 259 current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. |
260 aria-haspopup="listbox" | 260 createClusterMap(current_df, args[dict['name']], args[dict['html_resource']], args[dict['pdfexport']]) |
261 aria-expanded="false" | 261 |
262 > | 262 def vivax_contigs(args,dict): |
263 <div class="position-relative"> | 263 # argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6} |
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 |
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 #test_cluster(args,dict) |
266 <input type="text" | 266 #return; |
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 |
268 data-hotkey="s,/" | 268 #subprocess.call('echo $PATH',shell = True) |
269 name="q" | 269 #sys.exit(1) |
270 value="" | 270 |
271 placeholder="Search" | 271 vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax" |
272 data-unscoped-placeholder="Search GitHub" | 272 shutil.copyfile(args[dict['contigs']], args[dict['name']]+".fa") |
273 data-scoped-placeholder="Search" | 273 blastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/COGs.fas") |
274 autocapitalize="off" | 274 orthPresence_df = getCogsPresent(blastResult_df, args[dict['name']], vivaxPath+r"/Database/COGlist.txt") |
275 aria-autocomplete="list" | 275 |
276 aria-controls="jump-to-results" | 276 binBlastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/Bin_2.fas") |
277 aria-label="Search" | 277 binPresence_df = getCogsPresent(binBlastResult_df, args[dict['name']], vivaxPath+r"/Database/binlist.txt") |
278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=UBI6zrTC3YpC0k8lrlu6srLfkSoG1pT6oQPtlColDmhV/VRup2DMPG2/7aV0Ny9S/lUPp8loX+6gx+nMJGy0Tg==" | 278 cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True) |
279 spellcheck="false" | 279 |
280 autocomplete="off" | 280 fname = args[dict['html_resource']]+r"/"+ args[dict['name']]+"_cogspresent.csv" |
281 > | 281 cogPresence_df.to_csv(fname) |
282 <input type="hidden" class="js-site-search-type-field" name="type" > | 282 current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. |
283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> | 283 createClusterMap(current_df, args[dict['name']], args[dict['html_resource']], args[dict['pdfexport']]) |
284 | 284 createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']]) |
285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> | 285 |
286 | 286 |
287 <ul class="d-none js-jump-to-suggestions-template-container"> | 287 if __name__ == "__main__": |
288 | 288 sys.exit() |
289 | 289 |
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 |
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 |
292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> | 292 |
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> | |
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> | |
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> | |
296 </div> | |
297 | |
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"> | |
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"> | |
301 </div> | |
302 | |
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"> | |
304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> | |
305 In this repository | |
306 </span> | |
307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> | |
308 All GitHub | |
309 </span> | |
310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> | |
311 </div> | |
312 | |
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"> | |
314 Jump to | |
315 <span class="d-inline-block ml-1 v-align-middle">↵</span> | |
316 </div> | |
317 </a> | |
318 </li> | |
319 | |
320 </ul> | |
321 | |
322 <ul class="d-none js-jump-to-no-results-template-container"> | |
323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> | |
324 <span class="text-gray">No suggested jump to results</span> | |
325 </li> | |
326 </ul> | |
327 | |
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"> | |
329 | |
330 | |
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"> | |
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=""> | |
333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> | |
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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"><span class="pl-k">import</span> matplotlib <span class="pl-k">as</span> mpl</td> | |
799 </tr> | |
800 <tr> | |
801 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> | |
802 <td id="LC21" 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> | |
803 </tr> | |
804 <tr> | |
805 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> | |
806 <td id="LC22" class="blob-code blob-code-inner js-file-line"> | |
807 </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> subprocess</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> shutil</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> re</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> pandas <span class="pl-k">as</span> pd</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"><span class="pl-k">import</span> os</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"> | |
832 </td> | |
833 </tr> | |
834 <tr> | |
835 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> | |
836 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</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"> | |
841 </td> | |
842 </tr> | |
843 <tr> | |
844 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> | |
845 <td id="LC31" 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> | |
846 </tr> | |
847 <tr> | |
848 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> | |
849 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">from</span> matplotlib.patches <span class="pl-k">import</span> Patch</td> | |
850 </tr> | |
851 <tr> | |
852 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> | |
853 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> seaborn <span class="pl-k">as</span> sns</td> | |
854 </tr> | |
855 <tr> | |
856 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> | |
857 <td id="LC34" class="blob-code blob-code-inner js-file-line"> | |
858 </td> | |
859 </tr> | |
860 <tr> | |
861 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> | |
862 <td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">assembleWithVelvet</span>(<span class="pl-smi">name</span>, <span class="pl-smi">kmers</span>, <span class="pl-smi">inslen</span>, <span class="pl-smi">covcut</span>, <span class="pl-smi">fastq1name</span>,<span class="pl-smi">fastq2name</span>):</td> | |
863 </tr> | |
864 <tr> | |
865 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> | |
866 <td id="LC36" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"</span></td> | |
867 </tr> | |
868 <tr> | |
869 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> | |
870 <td id="LC37" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>velveth <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>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span> kmers<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> kmers <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span> -shortPaired -fastq <span class="pl-pds">"</span></span> <span class="pl-k">+</span> fastq1name<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>fastq2name</td> | |
871 </tr> | |
872 <tr> | |
873 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> | |
874 <td id="LC38" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> | |
875 </tr> | |
876 <tr> | |
877 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> | |
878 <td id="LC39" 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> | |
879 </tr> | |
880 <tr> | |
881 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> | |
882 <td id="LC40" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> | |
883 </tr> | |
884 <tr> | |
885 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> | |
886 <td id="LC41" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in velveth<span class="pl-pds">"</span></span></td> | |
887 </tr> | |
888 <tr> | |
889 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> | |
890 <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>velvetg <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>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -exp_cov auto -ins_length <span class="pl-pds">"</span></span><span class="pl-k">+</span>inslen<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -clean yes -ins_length_sd 50 -min_pair_count 20<span class="pl-pds">"</span></span></td> | |
891 </tr> | |
892 <tr> | |
893 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> | |
894 <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"</span></td> | |
895 </tr> | |
896 <tr> | |
897 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> | |
898 <td id="LC44" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString</span></td> | |
899 </tr> | |
900 <tr> | |
901 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> | |
902 <td id="LC45" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> | |
903 </tr> | |
904 <tr> | |
905 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> | |
906 <td id="LC46" 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> | |
907 </tr> | |
908 <tr> | |
909 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> | |
910 <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> | |
911 </tr> | |
912 <tr> | |
913 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> | |
914 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in velvetg<span class="pl-pds">"</span></span></td> | |
915 </tr> | |
916 <tr> | |
917 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> | |
918 <td id="LC49" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_k<span class="pl-pds">"</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>//contigs.fa<span class="pl-pds">"</span></span>,name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>.fa<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span> my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";</span></td> | |
919 </tr> | |
920 <tr> | |
921 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> | |
922 <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>ok<span class="pl-pds">"</span></span></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"> | |
927 </td> | |
928 </tr> | |
929 <tr> | |
930 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> | |
931 <td id="LC52" class="blob-code blob-code-inner js-file-line"> | |
932 </td> | |
933 </tr> | |
934 <tr> | |
935 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> | |
936 <td id="LC53" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">database</span>):</td> | |
937 </tr> | |
938 <tr> | |
939 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> | |
940 <td id="LC54" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(test_name)</td> | |
941 </tr> | |
942 <tr> | |
943 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> | |
944 <td id="LC55" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(database)</td> | |
945 </tr> | |
946 <tr> | |
947 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> | |
948 <td id="LC56" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>db_path = os.path.dirname(os.path.realpath(__file__))+database</span></td> | |
949 </tr> | |
950 <tr> | |
951 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> | |
952 <td id="LC57" class="blob-code blob-code-inner js-file-line"> db_path <span class="pl-k">=</span> database</td> | |
953 </tr> | |
954 <tr> | |
955 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> | |
956 <td id="LC58" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>blastn -db <span class="pl-pds">"</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -query <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.fa -outfmt 10 -out <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span></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"> <span class="pl-c1">print</span>(argString)</td> | |
961 </tr> | |
962 <tr> | |
963 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> | |
964 <td id="LC60" 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> | |
965 </tr> | |
966 <tr> | |
967 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> | |
968 <td id="LC61" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> | |
969 </tr> | |
970 <tr> | |
971 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> | |
972 <td id="LC62" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in blastall<span class="pl-pds">"</span></span></td> | |
973 </tr> | |
974 <tr> | |
975 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> | |
976 <td id="LC63" class="blob-code blob-code-inner js-file-line"> blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span>)</td> | |
977 </tr> | |
978 <tr> | |
979 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> | |
980 <td id="LC64" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (blast_df)</span></td> | |
981 </tr> | |
982 <tr> | |
983 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> | |
984 <td id="LC65" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){</span></td> | |
985 </tr> | |
986 <tr> | |
987 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> | |
988 <td id="LC66" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore'</span></td> | |
989 </tr> | |
990 <tr> | |
991 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> | |
992 <td id="LC67" class="blob-code blob-code-inner js-file-line"> blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>mismatch<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>gapopen<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qend<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>sstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>send<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]</td> | |
993 </tr> | |
994 <tr> | |
995 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> | |
996 <td id="LC68" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]<span class="pl-k">>=</span><span class="pl-c1">98</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">100</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>]<span class="pl-k"><</span><span class="pl-c1">0.001</span>) ]</td> | |
997 </tr> | |
998 <tr> | |
999 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> | |
1000 <td id="LC69" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]] <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td> | |
1001 </tr> | |
1002 <tr> | |
1003 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> | |
1004 <td id="LC70" class="blob-code blob-code-inner js-file-line"> | |
1005 </td> | |
1006 </tr> | |
1007 <tr> | |
1008 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> | |
1009 <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> blastResult_df</td> | |
1010 </tr> | |
1011 <tr> | |
1012 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> | |
1013 <td id="LC72" class="blob-code blob-code-inner js-file-line"> | |
1014 </td> | |
1015 </tr> | |
1016 <tr> | |
1017 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> | |
1018 <td id="LC73" class="blob-code blob-code-inner js-file-line"> | |
1019 </td> | |
1020 </tr> | |
1021 <tr> | |
1022 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> | |
1023 <td id="LC74" class="blob-code blob-code-inner js-file-line"> | |
1024 </td> | |
1025 </tr> | |
1026 <tr> | |
1027 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> | |
1028 <td id="LC75" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getCogsPresent</span>(<span class="pl-smi">blastResult_df</span>,<span class="pl-smi">strain</span>,<span class="pl-smi">cogOrBinList</span>):</td> | |
1029 </tr> | |
1030 <tr> | |
1031 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> | |
1032 <td id="LC76" class="blob-code blob-code-inner js-file-line"> blastResult_df.sort_values(<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>,<span class="pl-v">axis</span> <span class="pl-k">=</span> <span class="pl-c1">0</span>, <span class="pl-v">ascending</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1033 </tr> | |
1034 <tr> | |
1035 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> | |
1036 <td id="LC77" class="blob-code blob-code-inner js-file-line"> nodeList <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>].tolist()</td> | |
1037 </tr> | |
1038 <tr> | |
1039 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> | |
1040 <td id="LC78" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>].tolist()</td> | |
1041 </tr> | |
1042 <tr> | |
1043 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> | |
1044 <td id="LC79" class="blob-code blob-code-inner js-file-line"> cogSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(cogList) <span class="pl-c"><span class="pl-c">#</span>get unique values</span></td> | |
1045 </tr> | |
1046 <tr> | |
1047 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> | |
1048 <td id="LC80" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> <span class="pl-c1">sorted</span>(cogSet) <span class="pl-c"><span class="pl-c">#</span>sort them</span></td> | |
1049 </tr> | |
1050 <tr> | |
1051 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> | |
1052 <td id="LC81" class="blob-code blob-code-inner js-file-line"> | |
1053 </td> | |
1054 </tr> | |
1055 <tr> | |
1056 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> | |
1057 <td id="LC82" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (cogList)</span></td> | |
1058 </tr> | |
1059 <tr> | |
1060 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> | |
1061 <td id="LC83" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (len(cogList))</span></td> | |
1062 </tr> | |
1063 <tr> | |
1064 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> | |
1065 <td id="LC84" class="blob-code blob-code-inner js-file-line"> | |
1066 </td> | |
1067 </tr> | |
1068 <tr> | |
1069 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> | |
1070 <td id="LC85" class="blob-code blob-code-inner js-file-line"> thereList <span class="pl-k">=</span> []</td> | |
1071 </tr> | |
1072 <tr> | |
1073 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> | |
1074 <td id="LC86" class="blob-code blob-code-inner js-file-line"> dataList <span class="pl-k">=</span> []</td> | |
1075 </tr> | |
1076 <tr> | |
1077 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> | |
1078 <td id="LC87" 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> | |
1079 </tr> | |
1080 <tr> | |
1081 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> | |
1082 <td id="LC88" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> cogOrBinList</td> | |
1083 </tr> | |
1084 <tr> | |
1085 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> | |
1086 <td id="LC89" class="blob-code blob-code-inner js-file-line"> cnt <span class="pl-k">=</span> <span class="pl-c1">0</span></td> | |
1087 </tr> | |
1088 <tr> | |
1089 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> | |
1090 <td id="LC90" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span> (fname) <span class="pl-k">as</span> f:</td> | |
1091 </tr> | |
1092 <tr> | |
1093 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> | |
1094 <td id="LC91" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> line <span class="pl-k">in</span> f:</td> | |
1095 </tr> | |
1096 <tr> | |
1097 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> | |
1098 <td id="LC92" class="blob-code blob-code-inner js-file-line"> dataList.append(line.rstrip(<span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n\r</span> <span class="pl-pds">'</span></span>))</td> | |
1099 </tr> | |
1100 <tr> | |
1101 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td> | |
1102 <td id="LC93" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line.rstrip(<span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n\r</span> <span class="pl-pds">'</span></span>) <span class="pl-k">in</span> cogList:</td> | |
1103 </tr> | |
1104 <tr> | |
1105 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> | |
1106 <td id="LC94" class="blob-code blob-code-inner js-file-line"> thereList.append(<span class="pl-s"><span class="pl-pds">'</span>1<span class="pl-pds">'</span></span>)</td> | |
1107 </tr> | |
1108 <tr> | |
1109 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td> | |
1110 <td id="LC95" class="blob-code blob-code-inner js-file-line"> cnt <span class="pl-k">=</span> cnt<span class="pl-k">+</span><span class="pl-c1">1</span></td> | |
1111 </tr> | |
1112 <tr> | |
1113 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> | |
1114 <td id="LC96" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> | |
1115 </tr> | |
1116 <tr> | |
1117 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> | |
1118 <td id="LC97" class="blob-code blob-code-inner js-file-line"> thereList.append(<span class="pl-s"><span class="pl-pds">'</span>0<span class="pl-pds">'</span></span>)</td> | |
1119 </tr> | |
1120 <tr> | |
1121 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> | |
1122 <td id="LC98" class="blob-code blob-code-inner js-file-line"> | |
1123 </td> | |
1124 </tr> | |
1125 <tr> | |
1126 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> | |
1127 <td id="LC99" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (thereList)</span></td> | |
1128 </tr> | |
1129 <tr> | |
1130 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> | |
1131 <td id="LC100" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (cnt)</span></td> | |
1132 </tr> | |
1133 <tr> | |
1134 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> | |
1135 <td id="LC101" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">'</span>Cog<span class="pl-pds">'</span></span>: dataList, strain: thereList}</td> | |
1136 </tr> | |
1137 <tr> | |
1138 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> | |
1139 <td id="LC102" class="blob-code blob-code-inner js-file-line"> presence_df <span class="pl-k">=</span> pd.DataFrame(data)</td> | |
1140 </tr> | |
1141 <tr> | |
1142 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> | |
1143 <td id="LC103" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (presence_df)</span></td> | |
1144 </tr> | |
1145 <tr> | |
1146 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> | |
1147 <td id="LC104" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> presence_df</td> | |
1148 </tr> | |
1149 <tr> | |
1150 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> | |
1151 <td id="LC105" class="blob-code blob-code-inner js-file-line"> | |
1152 </td> | |
1153 </tr> | |
1154 <tr> | |
1155 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> | |
1156 <td id="LC106" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">addToCurrentData</span>(<span class="pl-smi">cog_df</span>, <span class="pl-smi">name</span>):</td> | |
1157 </tr> | |
1158 <tr> | |
1159 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> | |
1160 <td id="LC107" 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> | |
1161 </tr> | |
1162 <tr> | |
1163 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> | |
1164 <td id="LC108" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax/TvDatabase<span class="pl-c1">.</span>csv<span class="pl-pds">"</span></span></td> | |
1165 </tr> | |
1166 <tr> | |
1167 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> | |
1168 <td id="LC109" class="blob-code blob-code-inner js-file-line"> tv_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td> | |
1169 </tr> | |
1170 <tr> | |
1171 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> | |
1172 <td id="LC110" class="blob-code blob-code-inner js-file-line"> | |
1173 </td> | |
1174 </tr> | |
1175 <tr> | |
1176 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> | |
1177 <td id="LC111" class="blob-code blob-code-inner js-file-line"> cogList <span class="pl-k">=</span> cog_df[name].tolist()</td> | |
1178 </tr> | |
1179 <tr> | |
1180 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> | |
1181 <td id="LC112" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cogList.insert(0,'Test')</span></td> | |
1182 </tr> | |
1183 <tr> | |
1184 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> | |
1185 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (len(tv_df))</span></td> | |
1186 </tr> | |
1187 <tr> | |
1188 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> | |
1189 <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(len(cogList))</span></td> | |
1190 </tr> | |
1191 <tr> | |
1192 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> | |
1193 <td id="LC115" class="blob-code blob-code-inner js-file-line"> | |
1194 </td> | |
1195 </tr> | |
1196 <tr> | |
1197 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> | |
1198 <td id="LC116" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(cogList)</span></td> | |
1199 </tr> | |
1200 <tr> | |
1201 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> | |
1202 <td id="LC117" class="blob-code blob-code-inner js-file-line"> tv_df.loc[:,name]<span class="pl-k">=</span>cogList</td> | |
1203 </tr> | |
1204 <tr> | |
1205 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> | |
1206 <td id="LC118" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> tv_df</td> | |
1207 </tr> | |
1208 <tr> | |
1209 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> | |
1210 <td id="LC119" class="blob-code blob-code-inner js-file-line"> | |
1211 </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"> | |
1216 </td> | |
1217 </tr> | |
1218 <tr> | |
1219 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> | |
1220 <td id="LC121" class="blob-code blob-code-inner js-file-line"> | |
1221 </td> | |
1222 </tr> | |
1223 <tr> | |
1224 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> | |
1225 <td id="LC122" class="blob-code blob-code-inner js-file-line"> | |
1226 </td> | |
1227 </tr> | |
1228 <tr> | |
1229 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> | |
1230 <td id="LC123" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createClusterMap</span>(<span class="pl-smi">tv_df</span>,<span class="pl-smi">name</span>,<span class="pl-smi">html_path</span>,<span class="pl-smi">pdfExport</span>):</td> | |
1231 </tr> | |
1232 <tr> | |
1233 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> | |
1234 <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>Retrieve Data</span></td> | |
1235 </tr> | |
1236 <tr> | |
1237 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> | |
1238 <td id="LC125" 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> | |
1239 </tr> | |
1240 <tr> | |
1241 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> | |
1242 <td id="LC126" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax/geoTv<span class="pl-c1">.</span>csv<span class="pl-pds">"</span></span></td> | |
1243 </tr> | |
1244 <tr> | |
1245 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> | |
1246 <td id="LC127" class="blob-code blob-code-inner js-file-line"> geo_df <span class="pl-k">=</span> pd.read_csv(j_fname)</td> | |
1247 </tr> | |
1248 <tr> | |
1249 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> | |
1250 <td id="LC128" class="blob-code blob-code-inner js-file-line"> geo_df.loc[<span class="pl-c1">len</span>(geo_df)] <span class="pl-k">=</span>[name,name,<span class="pl-s"><span class="pl-pds">'</span>k<span class="pl-pds">'</span></span>]</td> | |
1251 </tr> | |
1252 <tr> | |
1253 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> | |
1254 <td id="LC129" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(geo_df)</td> | |
1255 </tr> | |
1256 <tr> | |
1257 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> | |
1258 <td id="LC130" class="blob-code blob-code-inner js-file-line"> | |
1259 </td> | |
1260 </tr> | |
1261 <tr> | |
1262 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> | |
1263 <td id="LC131" class="blob-code blob-code-inner js-file-line"> myStrains <span class="pl-k">=</span> tv_df.columns.values.tolist() <span class="pl-c"><span class="pl-c">#</span>beware first entry is COG</span></td> | |
1264 </tr> | |
1265 <tr> | |
1266 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> | |
1267 <td id="LC132" class="blob-code blob-code-inner js-file-line"> myStrains <span class="pl-k">=</span> myStrains[<span class="pl-c1">1</span>:]</td> | |
1268 </tr> | |
1269 <tr> | |
1270 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> | |
1271 <td id="LC133" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(myStrains)</td> | |
1272 </tr> | |
1273 <tr> | |
1274 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> | |
1275 <td id="LC134" class="blob-code blob-code-inner js-file-line"> myPal <span class="pl-k">=</span> []</td> | |
1276 </tr> | |
1277 <tr> | |
1278 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> | |
1279 <td id="LC135" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> s <span class="pl-k">in</span> myStrains:</td> | |
1280 </tr> | |
1281 <tr> | |
1282 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> | |
1283 <td id="LC136" class="blob-code blob-code-inner js-file-line"> col <span class="pl-k">=</span> geo_df[(geo_df[<span class="pl-s"><span class="pl-pds">'</span>Strain<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> s)][<span class="pl-s"><span class="pl-pds">'</span>colour<span class="pl-pds">'</span></span>].tolist()</td> | |
1284 </tr> | |
1285 <tr> | |
1286 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> | |
1287 <td id="LC137" class="blob-code blob-code-inner js-file-line"> myPal.append(col[<span class="pl-c1">0</span>])</td> | |
1288 </tr> | |
1289 <tr> | |
1290 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> | |
1291 <td id="LC138" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(myPal)</td> | |
1292 </tr> | |
1293 <tr> | |
1294 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> | |
1295 <td id="LC139" class="blob-code blob-code-inner js-file-line"> mycogmap <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>skyblue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>orangered<span class="pl-pds">'</span></span>] <span class="pl-c"><span class="pl-c">#</span> blue absent,red present</span></td> | |
1296 </tr> | |
1297 <tr> | |
1298 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> | |
1299 <td id="LC140" class="blob-code blob-code-inner js-file-line"> tv_df.set_index(<span class="pl-s"><span class="pl-pds">'</span>COG<span class="pl-pds">'</span></span>, <span class="pl-v">inplace</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1300 </tr> | |
1301 <tr> | |
1302 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> | |
1303 <td id="LC141" class="blob-code blob-code-inner js-file-line"> tv_df <span class="pl-k">=</span> tv_df[tv_df.columns].astype(<span class="pl-c1">float</span>)</td> | |
1304 </tr> | |
1305 <tr> | |
1306 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> | |
1307 <td id="LC142" class="blob-code blob-code-inner js-file-line"> | |
1308 </td> | |
1309 </tr> | |
1310 <tr> | |
1311 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td> | |
1312 <td id="LC143" class="blob-code blob-code-inner js-file-line"> cg <span class="pl-k">=</span> sns.clustermap(tv_df, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>ward<span class="pl-pds">'</span></span>, <span class="pl-v">col_colors</span><span class="pl-k">=</span>myPal, <span class="pl-v">cmap</span><span class="pl-k">=</span>mycogmap, <span class="pl-v">yticklabels</span> <span class="pl-k">=</span> <span class="pl-c1">1500</span>, <span class="pl-v">row_cluster</span><span class="pl-k">=</span><span class="pl-c1">False</span>, <span class="pl-v">linewidths</span> <span class="pl-k">=</span> <span class="pl-c1">0</span>)</td> | |
1313 </tr> | |
1314 <tr> | |
1315 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td> | |
1316 <td id="LC144" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cg = sns.clustermap(tv_df, method='ward', row_cluster=False, linewidths = 0)</span></td> | |
1317 </tr> | |
1318 <tr> | |
1319 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td> | |
1320 <td id="LC145" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td> | |
1321 </tr> | |
1322 <tr> | |
1323 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td> | |
1324 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>xasix ticks and labels.</span></td> | |
1325 </tr> | |
1326 <tr> | |
1327 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td> | |
1328 <td id="LC147" class="blob-code blob-code-inner js-file-line"> ax.xaxis.tick_top() <span class="pl-c"><span class="pl-c">#</span>set ticks at top</span></td> | |
1329 </tr> | |
1330 <tr> | |
1331 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td> | |
1332 <td id="LC148" class="blob-code blob-code-inner js-file-line"> newlabs <span class="pl-k">=</span> []</td> | |
1333 </tr> | |
1334 <tr> | |
1335 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td> | |
1336 <td id="LC149" class="blob-code blob-code-inner js-file-line"> | |
1337 </td> | |
1338 </tr> | |
1339 <tr> | |
1340 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td> | |
1341 <td id="LC150" class="blob-code blob-code-inner js-file-line"> labs <span class="pl-k">=</span> ax.xaxis.get_ticklabels()</td> | |
1342 </tr> | |
1343 <tr> | |
1344 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td> | |
1345 <td id="LC151" 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">len</span>(labs)):</td> | |
1346 </tr> | |
1347 <tr> | |
1348 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td> | |
1349 <td id="LC152" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(labs[i])</td> | |
1350 </tr> | |
1351 <tr> | |
1352 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td> | |
1353 <td id="LC153" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars</span></td> | |
1354 </tr> | |
1355 <tr> | |
1356 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td> | |
1357 <td id="LC154" class="blob-code blob-code-inner js-file-line"> newlabs.append(<span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span> <span class="pl-k">+</span> labs[i].get_text())</td> | |
1358 </tr> | |
1359 <tr> | |
1360 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td> | |
1361 <td id="LC155" class="blob-code blob-code-inner js-file-line"> ax.xaxis.set_ticklabels(newlabs)</td> | |
1362 </tr> | |
1363 <tr> | |
1364 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td> | |
1365 <td id="LC156" class="blob-code blob-code-inner js-file-line"> | |
1366 </td> | |
1367 </tr> | |
1368 <tr> | |
1369 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td> | |
1370 <td id="LC157" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>labs = ax.xaxis.get_ticklabels()</span></td> | |
1371 </tr> | |
1372 <tr> | |
1373 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td> | |
1374 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>for i in range(0, len(labs)):</span></td> | |
1375 </tr> | |
1376 <tr> | |
1377 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td> | |
1378 <td id="LC159" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(labs[i])</span></td> | |
1379 </tr> | |
1380 <tr> | |
1381 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td> | |
1382 <td id="LC160" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars</span></td> | |
1383 </tr> | |
1384 <tr> | |
1385 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td> | |
1386 <td id="LC161" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(labs[i])</span></td> | |
1387 </tr> | |
1388 <tr> | |
1389 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td> | |
1390 <td id="LC162" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ax.xaxis.set_ticklabels(labs)</span></td> | |
1391 </tr> | |
1392 <tr> | |
1393 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td> | |
1394 <td id="LC163" class="blob-code blob-code-inner js-file-line"> plt.setp(cg.ax_heatmap.xaxis.get_ticklabels(), <span class="pl-v">rotation</span><span class="pl-k">=</span><span class="pl-c1">90</span>) <span class="pl-c"><span class="pl-c">#</span> get x labels printed vertically</span></td> | |
1395 </tr> | |
1396 <tr> | |
1397 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td> | |
1398 <td id="LC164" class="blob-code blob-code-inner js-file-line"> | |
1399 </td> | |
1400 </tr> | |
1401 <tr> | |
1402 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td> | |
1403 <td id="LC165" class="blob-code blob-code-inner js-file-line"> cg.cax.set_visible(<span class="pl-c1">False</span>)</td> | |
1404 </tr> | |
1405 <tr> | |
1406 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td> | |
1407 <td id="LC166" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td> | |
1408 </tr> | |
1409 <tr> | |
1410 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td> | |
1411 <td id="LC167" class="blob-code blob-code-inner js-file-line"> ax.set_yticklabels(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span>)</td> | |
1412 </tr> | |
1413 <tr> | |
1414 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td> | |
1415 <td id="LC168" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span>)</td> | |
1416 </tr> | |
1417 <tr> | |
1418 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td> | |
1419 <td id="LC169" class="blob-code blob-code-inner js-file-line"> ax <span class="pl-k">=</span> cg.ax_heatmap</td> | |
1420 </tr> | |
1421 <tr> | |
1422 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td> | |
1423 <td id="LC170" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> ax.set_title("Variant antigen profiles of T. vivax genomes.\nDendrogram reflects the VSG repertoire relationships of each strain inferred by the presence and absence of non-universal T. vivax VSG orthologs.", va = "top", wrap = "True")</span></td> | |
1424 </tr> | |
1425 <tr> | |
1426 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td> | |
1427 <td id="LC171" class="blob-code blob-code-inner js-file-line"> b <span class="pl-k">=</span> <span class="pl-c1">len</span>(tv_df)</td> | |
1428 </tr> | |
1429 <tr> | |
1430 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td> | |
1431 <td id="LC172" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(b)</td> | |
1432 </tr> | |
1433 <tr> | |
1434 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td> | |
1435 <td id="LC173" 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 Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ <span class="pl-pds">"</span></span> \</td> | |
1436 </tr> | |
1437 <tr> | |
1438 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td> | |
1439 <td id="LC174" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>showing the <span class="pl-cce">\n</span>combination of present and absent diagnostic cluster of VSG orthologs <span class="pl-pds">"</span></span> \</td> | |
1440 </tr> | |
1441 <tr> | |
1442 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td> | |
1443 <td id="LC175" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>across the sample cohort. <span class="pl-cce">\n</span>Dendrogram reflects the relationships amongst the VSG<span class="pl-pds">"</span></span> \</td> | |
1444 </tr> | |
1445 <tr> | |
1446 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td> | |
1447 <td id="LC176" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span> repertoires of each strain. <span class="pl-pds">"</span></span> \</td> | |
1448 </tr> | |
1449 <tr> | |
1450 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td> | |
1451 <td id="LC177" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Strains were isolated <span class="pl-cce">\n</span>from multiple African countries as shown in the key.<span class="pl-cce">\n</span>Data was produced with the <span class="pl-pds">"</span></span> \</td> | |
1452 </tr> | |
1453 <tr> | |
1454 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td> | |
1455 <td id="LC178" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>'Variant Antigen Profiler' (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> | |
1456 </tr> | |
1457 <tr> | |
1458 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td> | |
1459 <td id="LC179" class="blob-code blob-code-inner js-file-line"> | |
1460 </td> | |
1461 </tr> | |
1462 <tr> | |
1463 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td> | |
1464 <td id="LC180" class="blob-code blob-code-inner js-file-line"> ax.text(<span class="pl-k">-</span><span class="pl-c1">1.5</span>, <span class="pl-c1">len</span>(tv_df) <span class="pl-k">+</span> <span class="pl-c1">8</span>,</td> | |
1465 </tr> | |
1466 <tr> | |
1467 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td> | |
1468 <td id="LC181" class="blob-code blob-code-inner js-file-line"> title,</td> | |
1469 </tr> | |
1470 <tr> | |
1471 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td> | |
1472 <td id="LC182" class="blob-code blob-code-inner js-file-line"> <span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>left<span class="pl-pds">"</span></span>, <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> | |
1473 </tr> | |
1474 <tr> | |
1475 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td> | |
1476 <td id="LC183" class="blob-code blob-code-inner js-file-line"> col <span class="pl-k">=</span> cg.ax_col_dendrogram.get_position()</td> | |
1477 </tr> | |
1478 <tr> | |
1479 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td> | |
1480 <td id="LC184" class="blob-code blob-code-inner js-file-line"> cg.ax_col_dendrogram.set_position([col.x0, col.y0<span class="pl-k">*</span><span class="pl-c1">1.08</span>, col.width, col.height<span class="pl-k">*</span><span class="pl-c1">1.1</span>])</td> | |
1481 </tr> | |
1482 <tr> | |
1483 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td> | |
1484 <td id="LC185" class="blob-code blob-code-inner js-file-line"> | |
1485 </td> | |
1486 </tr> | |
1487 <tr> | |
1488 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td> | |
1489 <td id="LC186" class="blob-code blob-code-inner js-file-line"> countryList <span class="pl-k">=</span> pd.unique(geo_df[<span class="pl-s"><span class="pl-pds">'</span>Location<span class="pl-pds">'</span></span>])</td> | |
1490 </tr> | |
1491 <tr> | |
1492 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td> | |
1493 <td id="LC187" class="blob-code blob-code-inner js-file-line"> colourList <span class="pl-k">=</span> pd.unique(geo_df[<span class="pl-s"><span class="pl-pds">'</span>colour<span class="pl-pds">'</span></span>])</td> | |
1494 </tr> | |
1495 <tr> | |
1496 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td> | |
1497 <td id="LC188" class="blob-code blob-code-inner js-file-line"> legend_elements <span class="pl-k">=</span> [Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>orangered<span class="pl-pds">'</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>COG Present<span class="pl-pds">'</span></span>),</td> | |
1498 </tr> | |
1499 <tr> | |
1500 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td> | |
1501 <td id="LC189" class="blob-code blob-code-inner js-file-line"> Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>skyblue<span class="pl-pds">'</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>COG Absent<span class="pl-pds">'</span></span>)]</td> | |
1502 </tr> | |
1503 <tr> | |
1504 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td> | |
1505 <td id="LC190" class="blob-code blob-code-inner js-file-line"> | |
1506 </td> | |
1507 </tr> | |
1508 <tr> | |
1509 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td> | |
1510 <td id="LC191" 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">len</span>(colourList)):</td> | |
1511 </tr> | |
1512 <tr> | |
1513 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td> | |
1514 <td id="LC192" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>country = <span class="pl-c1">%s</span>, colour = <span class="pl-c1">%s</span><span class="pl-pds">"</span></span> <span class="pl-k">%</span> (countryList[i], colourList[i]))</td> | |
1515 </tr> | |
1516 <tr> | |
1517 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td> | |
1518 <td id="LC193" class="blob-code blob-code-inner js-file-line"> p <span class="pl-k">=</span> Patch(<span class="pl-v">facecolor</span><span class="pl-k">=</span><span class="pl-c1">str</span>(colourList[i]), <span class="pl-v">label</span><span class="pl-k">=</span>countryList[i])</td> | |
1519 </tr> | |
1520 <tr> | |
1521 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td> | |
1522 <td id="LC194" class="blob-code blob-code-inner js-file-line"> legend_elements.append(p)</td> | |
1523 </tr> | |
1524 <tr> | |
1525 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td> | |
1526 <td id="LC195" class="blob-code blob-code-inner js-file-line"> | |
1527 </td> | |
1528 </tr> | |
1529 <tr> | |
1530 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td> | |
1531 <td id="LC196" class="blob-code blob-code-inner js-file-line"> ax.legend(<span class="pl-v">handles</span> <span class="pl-k">=</span> legend_elements, <span class="pl-v">bbox_to_anchor</span><span class="pl-k">=</span>(<span class="pl-k">-</span><span class="pl-c1">0.3</span>,<span class="pl-c1">1.2</span>),<span class="pl-v">loc</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>upper left<span class="pl-pds">'</span></span>)</td> | |
1532 </tr> | |
1533 <tr> | |
1534 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td> | |
1535 <td id="LC197" class="blob-code blob-code-inner js-file-line"> | |
1536 </td> | |
1537 </tr> | |
1538 <tr> | |
1539 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td> | |
1540 <td id="LC198" class="blob-code blob-code-inner js-file-line"> | |
1541 </td> | |
1542 </tr> | |
1543 <tr> | |
1544 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td> | |
1545 <td id="LC199" class="blob-code blob-code-inner js-file-line"> | |
1546 </td> | |
1547 </tr> | |
1548 <tr> | |
1549 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td> | |
1550 <td id="LC200" class="blob-code blob-code-inner js-file-line"> | |
1551 </td> | |
1552 </tr> | |
1553 <tr> | |
1554 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td> | |
1555 <td id="LC201" class="blob-code blob-code-inner js-file-line"> | |
1556 </td> | |
1557 </tr> | |
1558 <tr> | |
1559 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td> | |
1560 <td id="LC202" class="blob-code blob-code-inner js-file-line"> | |
1561 </td> | |
1562 </tr> | |
1563 <tr> | |
1564 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td> | |
1565 <td id="LC203" class="blob-code blob-code-inner js-file-line"> | |
1566 </td> | |
1567 </tr> | |
1568 <tr> | |
1569 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td> | |
1570 <td id="LC204" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0 ) # get y labels printed horizontally</span></td> | |
1571 </tr> | |
1572 <tr> | |
1573 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td> | |
1574 <td id="LC205" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_col.linkage # linkage matrix for columns</span></td> | |
1575 </tr> | |
1576 <tr> | |
1577 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td> | |
1578 <td id="LC206" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> cg.dendrogram_row.linkage # linkage matrix for rows</span></td> | |
1579 </tr> | |
1580 <tr> | |
1581 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td> | |
1582 <td id="LC207" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.savefig(r"results/" + name + "_heatmap.png")</span></td> | |
1583 </tr> | |
1584 <tr> | |
1585 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td> | |
1586 <td id="LC208" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.savefig(htmlresource + "/heatmap.png")</span></td> | |
1587 </tr> | |
1588 <tr> | |
1589 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td> | |
1590 <td id="LC209" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>if pdf == 'PDF_Yes':</span></td> | |
1591 </tr> | |
1592 <tr> | |
1593 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td> | |
1594 <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.savefig(htmlresource + "/heatmap.pdf")</span></td> | |
1595 </tr> | |
1596 <tr> | |
1597 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td> | |
1598 <td id="LC211" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> shutil.copyfile("heatmap.pdf",heatmapfn) #</span></td> | |
1599 </tr> | |
1600 <tr> | |
1601 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td> | |
1602 <td id="LC212" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.legend()</span></td> | |
1603 </tr> | |
1604 <tr> | |
1605 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td> | |
1606 <td id="LC213" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> html_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>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_clustermap.png<span class="pl-pds">"</span></span></td> | |
1607 </tr> | |
1608 <tr> | |
1609 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td> | |
1610 <td id="LC214" class="blob-code blob-code-inner js-file-line"> cg.savefig(fname)</td> | |
1611 </tr> | |
1612 <tr> | |
1613 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td> | |
1614 <td id="LC215" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> pdfExport <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td> | |
1615 </tr> | |
1616 <tr> | |
1617 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td> | |
1618 <td id="LC216" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> html_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> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>_clustermap.pdf<span class="pl-pds">"</span></span></td> | |
1619 </tr> | |
1620 <tr> | |
1621 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td> | |
1622 <td id="LC217" class="blob-code blob-code-inner js-file-line"> cg.savefig(fname)</td> | |
1623 </tr> | |
1624 <tr> | |
1625 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td> | |
1626 <td id="LC218" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td> | |
1627 </tr> | |
1628 <tr> | |
1629 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td> | |
1630 <td id="LC219" class="blob-code blob-code-inner js-file-line"> | |
1631 </td> | |
1632 </tr> | |
1633 <tr> | |
1634 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td> | |
1635 <td id="LC220" 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">htmlPath</span>):</td> | |
1636 </tr> | |
1637 <tr> | |
1638 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td> | |
1639 <td id="LC221" 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> | |
1640 </tr> | |
1641 <tr> | |
1642 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td> | |
1643 <td id="LC222" 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>vivax VAP</title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td> | |
1644 </tr> | |
1645 <tr> | |
1646 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td> | |
1647 <td id="LC223" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> name</td> | |
1648 </tr> | |
1649 <tr> | |
1650 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td> | |
1651 <td id="LC224" class="blob-code blob-code-inner js-file-line"> | |
1652 </td> | |
1653 </tr> | |
1654 <tr> | |
1655 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td> | |
1656 <td id="LC225" class="blob-code blob-code-inner js-file-line"> | |
1657 </td> | |
1658 </tr> | |
1659 <tr> | |
1660 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td> | |
1661 <td id="LC226" 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>The Heat Map and Dendrogram</h3></p><span class="pl-pds">'</span></span></td> | |
1662 </tr> | |
1663 <tr> | |
1664 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td> | |
1665 <td id="LC227" 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 = '<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>_clustermap.png' alt='Cog Clustermap' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> | |
1666 </tr> | |
1667 <tr> | |
1668 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td> | |
1669 <td id="LC228" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> | |
1670 </tr> | |
1671 <tr> | |
1672 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td> | |
1673 <td id="LC229" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(htmlString)</td> | |
1674 </tr> | |
1675 <tr> | |
1676 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td> | |
1677 <td id="LC230" class="blob-code blob-code-inner js-file-line"> | |
1678 </td> | |
1679 </tr> | |
1680 <tr> | |
1681 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td> | |
1682 <td id="LC231" 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> | |
1683 </tr> | |
1684 <tr> | |
1685 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td> | |
1686 <td id="LC232" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> | |
1687 </tr> | |
1688 <tr> | |
1689 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td> | |
1690 <td id="LC233" class="blob-code blob-code-inner js-file-line"> | |
1691 </td> | |
1692 </tr> | |
1693 <tr> | |
1694 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td> | |
1695 <td id="LC234" class="blob-code blob-code-inner js-file-line"> | |
1696 </td> | |
1697 </tr> | |
1698 <tr> | |
1699 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td> | |
1700 <td id="LC235" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">vivax_assemble</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td> | |
1701 </tr> | |
1702 <tr> | |
1703 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td> | |
1704 <td id="LC236" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10}</span></td> | |
1705 </tr> | |
1706 <tr> | |
1707 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td> | |
1708 <td id="LC237" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assembleWithVelvet("V2_Test", '65', '400', '5', "data/TviBrRp.1.clean", "data/TviBrRp.2.clean")</span></td> | |
1709 </tr> | |
1710 <tr> | |
1711 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td> | |
1712 <td id="LC238" class="blob-code blob-code-inner js-file-line"> | |
1713 </td> | |
1714 </tr> | |
1715 <tr> | |
1716 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td> | |
1717 <td id="LC239" class="blob-code blob-code-inner js-file-line"> vivaxPath <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax<span class="pl-pds">"</span></span></td> | |
1718 </tr> | |
1719 <tr> | |
1720 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td> | |
1721 <td id="LC240" class="blob-code blob-code-inner js-file-line"> assembleWithVelvet(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>kmers<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>inslen<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>covcut<span class="pl-pds">'</span></span>]],</td> | |
1722 </tr> | |
1723 <tr> | |
1724 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td> | |
1725 <td id="LC241" class="blob-code blob-code-inner js-file-line"> 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>]])</td> | |
1726 </tr> | |
1727 <tr> | |
1728 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td> | |
1729 <td id="LC242" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td> | |
1730 </tr> | |
1731 <tr> | |
1732 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td> | |
1733 <td id="LC243" class="blob-code blob-code-inner js-file-line"> orthPresence_df <span class="pl-k">=</span> getCogsPresent(blastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td> | |
1734 </tr> | |
1735 <tr> | |
1736 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td> | |
1737 <td id="LC244" class="blob-code blob-code-inner js-file-line"> | |
1738 </td> | |
1739 </tr> | |
1740 <tr> | |
1741 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td> | |
1742 <td id="LC245" class="blob-code blob-code-inner js-file-line"> binBlastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td> | |
1743 </tr> | |
1744 <tr> | |
1745 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td> | |
1746 <td id="LC246" class="blob-code blob-code-inner js-file-line"> binPresence_df <span class="pl-k">=</span> getCogsPresent(binBlastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td> | |
1747 </tr> | |
1748 <tr> | |
1749 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td> | |
1750 <td id="LC247" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> orthPresence_df.append(binPresence_df, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1751 </tr> | |
1752 <tr> | |
1753 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td> | |
1754 <td id="LC248" class="blob-code blob-code-inner js-file-line"> | |
1755 </td> | |
1756 </tr> | |
1757 <tr> | |
1758 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td> | |
1759 <td id="LC249" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]] <span class="pl-k">+</span>args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_cogspresent.csv<span class="pl-pds">"</span></span></td> | |
1760 </tr> | |
1761 <tr> | |
1762 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td> | |
1763 <td id="LC250" class="blob-code blob-code-inner js-file-line"> cogPresence_df.to_csv(fname)</td> | |
1764 </tr> | |
1765 <tr> | |
1766 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td> | |
1767 <td id="LC251" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,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> load in Tvdatabase and add cogPresence column to it.</span></td> | |
1768 </tr> | |
1769 <tr> | |
1770 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td> | |
1771 <td id="LC252" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, 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>]],args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td> | |
1772 </tr> | |
1773 <tr> | |
1774 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td> | |
1775 <td id="LC253" 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>]])</td> | |
1776 </tr> | |
1777 <tr> | |
1778 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td> | |
1779 <td id="LC254" class="blob-code blob-code-inner js-file-line"> | |
1780 </td> | |
1781 </tr> | |
1782 <tr> | |
1783 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td> | |
1784 <td id="LC255" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">test_cluster</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td> | |
1785 </tr> | |
1786 <tr> | |
1787 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td> | |
1788 <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span> (<span class="pl-s"><span class="pl-pds">"</span>name: <span class="pl-c1">%s</span><span class="pl-pds">"</span></span>,args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]])</td> | |
1789 </tr> | |
1790 <tr> | |
1791 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td> | |
1792 <td id="LC257" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span>test_cogspresent.csv<span class="pl-pds">"</span></span>)</td> | |
1793 </tr> | |
1794 <tr> | |
1795 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td> | |
1796 <td id="LC258" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(cogPresence_df)</td> | |
1797 </tr> | |
1798 <tr> | |
1799 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td> | |
1800 <td id="LC259" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,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> load in Tvdatabase and add cogPresence column to it.</span></td> | |
1801 </tr> | |
1802 <tr> | |
1803 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td> | |
1804 <td id="LC260" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, 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>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td> | |
1805 </tr> | |
1806 <tr> | |
1807 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td> | |
1808 <td id="LC261" class="blob-code blob-code-inner js-file-line"> | |
1809 </td> | |
1810 </tr> | |
1811 <tr> | |
1812 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td> | |
1813 <td id="LC262" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">vivax_contigs</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td> | |
1814 </tr> | |
1815 <tr> | |
1816 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td> | |
1817 <td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6}</span></td> | |
1818 </tr> | |
1819 <tr> | |
1820 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td> | |
1821 <td id="LC264" class="blob-code blob-code-inner js-file-line"> | |
1822 </td> | |
1823 </tr> | |
1824 <tr> | |
1825 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td> | |
1826 <td id="LC265" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>test_cluster(args,dict)</span></td> | |
1827 </tr> | |
1828 <tr> | |
1829 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td> | |
1830 <td id="LC266" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>return;</span></td> | |
1831 </tr> | |
1832 <tr> | |
1833 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td> | |
1834 <td id="LC267" class="blob-code blob-code-inner js-file-line"> | |
1835 </td> | |
1836 </tr> | |
1837 <tr> | |
1838 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td> | |
1839 <td id="LC268" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>subprocess.call('echo $PATH',shell = True)</span></td> | |
1840 </tr> | |
1841 <tr> | |
1842 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td> | |
1843 <td id="LC269" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>sys.exit(1)</span></td> | |
1844 </tr> | |
1845 <tr> | |
1846 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td> | |
1847 <td id="LC270" class="blob-code blob-code-inner js-file-line"> | |
1848 </td> | |
1849 </tr> | |
1850 <tr> | |
1851 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td> | |
1852 <td id="LC271" class="blob-code blob-code-inner js-file-line"> vivaxPath <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/data/vivax<span class="pl-pds">"</span></span></td> | |
1853 </tr> | |
1854 <tr> | |
1855 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td> | |
1856 <td id="LC272" class="blob-code blob-code-inner js-file-line"> shutil.copyfile(args[dict[<span class="pl-s"><span class="pl-pds">'</span>contigs<span class="pl-pds">'</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.fa<span class="pl-pds">"</span></span>)</td> | |
1857 </tr> | |
1858 <tr> | |
1859 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td> | |
1860 <td id="LC273" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td> | |
1861 </tr> | |
1862 <tr> | |
1863 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td> | |
1864 <td id="LC274" class="blob-code blob-code-inner js-file-line"> orthPresence_df <span class="pl-k">=</span> getCogsPresent(blastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td> | |
1865 </tr> | |
1866 <tr> | |
1867 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td> | |
1868 <td id="LC275" class="blob-code blob-code-inner js-file-line"> | |
1869 </td> | |
1870 </tr> | |
1871 <tr> | |
1872 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td> | |
1873 <td id="LC276" class="blob-code blob-code-inner js-file-line"> binBlastResult_df <span class="pl-k">=</span> blastContigs(args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">"</span></span>)</td> | |
1874 </tr> | |
1875 <tr> | |
1876 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td> | |
1877 <td id="LC277" class="blob-code blob-code-inner js-file-line"> binPresence_df <span class="pl-k">=</span> getCogsPresent(binBlastResult_df, args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">"</span></span>)</td> | |
1878 </tr> | |
1879 <tr> | |
1880 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td> | |
1881 <td id="LC278" class="blob-code blob-code-inner js-file-line"> cogPresence_df <span class="pl-k">=</span> orthPresence_df.append(binPresence_df, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> | |
1882 </tr> | |
1883 <tr> | |
1884 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td> | |
1885 <td id="LC279" class="blob-code blob-code-inner js-file-line"> | |
1886 </td> | |
1887 </tr> | |
1888 <tr> | |
1889 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td> | |
1890 <td id="LC280" class="blob-code blob-code-inner js-file-line"> fname <span class="pl-k">=</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span> args[dict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_cogspresent.csv<span class="pl-pds">"</span></span></td> | |
1891 </tr> | |
1892 <tr> | |
1893 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td> | |
1894 <td id="LC281" class="blob-code blob-code-inner js-file-line"> cogPresence_df.to_csv(fname)</td> | |
1895 </tr> | |
1896 <tr> | |
1897 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td> | |
1898 <td id="LC282" class="blob-code blob-code-inner js-file-line"> current_df <span class="pl-k">=</span> addToCurrentData(cogPresence_df,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> load in Tvdatabase and add cogPresence column to it.</span></td> | |
1899 </tr> | |
1900 <tr> | |
1901 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td> | |
1902 <td id="LC283" class="blob-code blob-code-inner js-file-line"> createClusterMap(current_df, 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>]], args[dict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]])</td> | |
1903 </tr> | |
1904 <tr> | |
1905 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td> | |
1906 <td id="LC284" 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>]])</td> | |
1907 </tr> | |
1908 <tr> | |
1909 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td> | |
1910 <td id="LC285" class="blob-code blob-code-inner js-file-line"> | |
1911 </td> | |
1912 </tr> | |
1913 <tr> | |
1914 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td> | |
1915 <td id="LC286" class="blob-code blob-code-inner js-file-line"> | |
1916 </td> | |
1917 </tr> | |
1918 <tr> | |
1919 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td> | |
1920 <td id="LC287" 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> | |
1921 </tr> | |
1922 <tr> | |
1923 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td> | |
1924 <td id="LC288" class="blob-code blob-code-inner js-file-line"> sys.exit()</td> | |
1925 </tr> | |
1926 <tr> | |
1927 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td> | |
1928 <td id="LC289" class="blob-code blob-code-inner js-file-line"> | |
1929 </td> | |
1930 </tr> | |
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1932 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td> | |
1933 <td id="LC290" class="blob-code blob-code-inner js-file-line"> | |
1934 </td> | |
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1938 <td id="LC291" class="blob-code blob-code-inner js-file-line"> | |
1939 </td> | |
1940 </tr> | |
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