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comparison Tryp_V.py @ 8:e75a85590041 draft

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author johnheap
date Mon, 03 Jun 2019 14:09:07 -0400
parents 4432e4183ebd
children e7da2274c9f6
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7:25226d33642e 8:e75a85590041
1 """ 1
2 * Copyright 2018 University of Liverpool 2
3 * Author: John Heap, Computational Biology Facility, UoL 3
4 * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL 4
5 * 5
6 * Licensed under the Apache License, Version 2.0 (the "License"); 6
7 * you may not use this file except in compliance with the License. 7 <!DOCTYPE html>
8 * You may obtain a copy of the License at 8 <html lang="en">
9 * 9 <head>
10 * http://www.apache.org/licenses/LICENSE-2.0 10 <meta charset="utf-8">
11 * 11 <link rel="dns-prefetch" href="https://github.githubassets.com">
12 * Unless required by applicable law or agreed to in writing, software 12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com">
13 * distributed under the License is distributed on an "AS IS" BASIS, 13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com">
14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com">
15 * See the License for the specific language governing permissions and 15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com">
16 * limitations under the License. 16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com">
17 * 17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/">
18 """ 18
19 19
20 import matplotlib as mpl 20
21 mpl.use('Agg') 21 <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" />
22 22 <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" />
23 import subprocess 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" />
24 import shutil 24
25 import re 25
26 import pandas as pd 26
27 import os 27
28 28
29 import sys 29 <meta name="viewport" content="width=device-width">
30 30
31 import matplotlib.pyplot as plt 31 <title>VAPPER-Galaxy/Tryp_V.py at master · johnheap/VAPPER-Galaxy · GitHub</title>
32 from matplotlib.patches import Patch 32 <meta name="description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub.">
33 import seaborn as sns 33 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
34 34 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub">
35 def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name): 35 <meta property="fb:app_id" content="1401488693436528">
36 #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq" 36
37 argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name 37 <meta name="twitter:image:src" content="https://avatars0.githubusercontent.com/u/24318980?s=400&amp;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." />
38 print(argString) 38 <meta property="og:image" content="https://avatars0.githubusercontent.com/u/24318980?s=400&amp;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." />
39 returncode = subprocess.call(argString, shell=True) 39
40 if returncode != 0: 40 <link rel="assets" href="https://github.githubassets.com/">
41 return "Error in velveth" 41
42 argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -clean yes -ins_length_sd 50 -min_pair_count 20" 42 <meta name="pjax-timeout" content="1000">
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" 43
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 44 <meta name="request-id" content="99EA:03C4:48319:89CA2:5CF56242" data-pjax-transient>
45 print(argString) 45
46 returncode = subprocess.call(argString, shell = True) 46
47 if returncode != 0: 47
48 return "Error in velvetg" 48
49 shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa") # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa"; 49 <meta name="selected-link" value="repo_source" data-pjax-transient>
50 return "ok" 50
51 51 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU">
52 52 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA">
53 def blastContigs(test_name,database): 53 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc">
54 print(test_name) 54
55 print(database) 55 <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="99EA:03C4:48319:89CA2:5CF56242" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" />
56 #db_path = os.path.dirname(os.path.realpath(__file__))+database 56 <meta name="analytics-location" content="/&lt;user-name&gt;/&lt;repo-name&gt;/blob/show" data-pjax-transient="true" />
57 db_path = database 57
58 argString = "blastn -db "+db_path+" -query "+test_name+".fa -outfmt 10 -out "+test_name+"_blast.txt" 58
59 print (argString) 59
60 returncode = subprocess.call(argString, shell = True) 60 <meta name="google-analytics" content="UA-3769691-2">
61 if returncode != 0: 61
62 return "Error in blastall" 62
63 blast_df = pd.read_csv(""+test_name+"_blast.txt") 63 <meta class="js-ga-set" name="dimension1" content="Logged Out">
64 #print (blast_df) 64
65 #if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){ 65
66 #'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore' 66
67 blast_df.columns = ['qaccver', 'saccver', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue','bitscore'] 67
68 blastResult_df = blast_df[(blast_df['pident']>=98) & (blast_df['length'] > 100) & (blast_df['evalue']<0.001) ] 68
69 blastResult_df = blastResult_df[['qaccver', 'saccver', 'pident']] #query accession.version, subject accession.version, Percentage of identical matches 69 <meta name="hostname" content="github.com">
70 70 <meta name="user-login" content="">
71 return blastResult_df 71
72 72 <meta name="expected-hostname" content="github.com">
73 73 <meta name="js-proxy-site-detection-payload" content="YzYyMzAwYTYwMTZlZjQ5YWUzNGIzNTY5ZmQ2NTkxYTVmNWQzYzA5NjdiMTY5MDUxNDBjODNkMjI2NjY2NDk3Znx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiI5OUVBOjAzQzQ6NDgzMTk6ODlDQTI6NUNGNTYyNDIiLCJ0aW1lc3RhbXAiOjE1NTk1ODUzNDYsImhvc3QiOiJnaXRodWIuY29tIn0=">
74 74
75 def getCogsPresent(blastResult_df,strain,cogOrBinList): 75 <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS">
76 blastResult_df.sort_values('pident',axis = 0, ascending=False, inplace=True) 76
77 nodeList = blastResult_df['qaccver'].tolist() 77 <meta name="html-safe-nonce" content="8f60f90a25489bbe59ea08995f73407524f71ec9">
78 cogList = blastResult_df['saccver'].tolist() 78
79 cogSet = set(cogList) #get unique values 79 <meta http-equiv="x-pjax-version" content="af1499c2254d0582d0a98af1dfd7f11b">
80 cogList = sorted(cogSet) #sort them 80
81 81
82 #print (cogList) 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">
83 #print (len(cogList)) 83
84 84 <meta name="go-import" content="github.com/johnheap/VAPPER-Galaxy git https://github.com/johnheap/VAPPER-Galaxy.git">
85 thereList = [] 85
86 dataList = [] 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" />
87 #dir_path = os.path.dirname(os.path.realpath(__file__)) 87
88 fname = cogOrBinList 88
89 cnt = 0 89 <link rel="canonical" href="https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py" data-pjax-transient>
90 with open (fname) as f: 90
91 for line in f: 91
92 dataList.append(line.rstrip('\n\r ')) 92 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats">
93 if line.rstrip('\n\r ') in cogList: 93
94 thereList.append('1') 94 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors">
95 cnt = cnt+1 95
96 else: 96 <link rel="mask-icon" href="https://github.githubassets.com/pinned-octocat.svg" color="#000000">
97 thereList.append('0') 97 <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://github.githubassets.com/favicon.ico">
98 98
99 #print (thereList) 99 <meta name="theme-color" content="#1e2327">
100 #print (cnt) 100
101 data = {'Cog': dataList, strain: thereList} 101
102 presence_df = pd.DataFrame(data) 102
103 #print (presence_df) 103
104 return presence_df 104
105 105 <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials">
106 def addToCurrentData(cog_df, name): 106
107 dir_path = os.path.dirname(os.path.realpath(__file__)) 107 </head>
108 j_fname = dir_path + r"/data/vivax/TvDatabase.csv" 108
109 tv_df = pd.read_csv(j_fname) 109 <body class="logged-out env-production page-responsive page-blob">
110 110
111 cogList = cog_df[name].tolist() 111
112 #cogList.insert(0,'Test') 112 <div class="position-relative js-header-wrapper ">
113 #print (len(tv_df)) 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>
114 #print(len(cogList)) 114 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div>
115 115
116 #print(cogList) 116
117 tv_df.loc[:,name]=cogList 117
118 return tv_df 118
119 119
120 120
121 121 <header class="Header-old header-logged-out js-details-container Details position-relative f4 py-2" role="banner">
122 122 <div class="container-lg d-lg-flex flex-items-center p-responsive">
123 def createClusterMap(tv_df,name,html_path,pdfExport): 123 <div class="d-flex flex-justify-between flex-items-center">
124 #Retrieve Data 124 <a class="mr-4" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
125 dir_path = os.path.dirname(os.path.realpath(__file__)) 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>
126 j_fname = dir_path+r"/data/vivax/geoTv.csv" 126 </a>
127 geo_df = pd.read_csv(j_fname) 127
128 geo_df.loc[len(geo_df)] =[name,name,'k'] 128 <div class="d-lg-none css-truncate css-truncate-target width-fit p-2">
129 print(geo_df) 129
130 130 <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>
131 myStrains = tv_df.columns.values.tolist() #beware first entry is COG 131 <a class="Header-link" href="/johnheap">johnheap</a>
132 myStrains = myStrains[1:] 132 /
133 print(myStrains) 133 <a class="Header-link" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a>
134 myPal = [] 134
135 for s in myStrains: 135
136 col = geo_df[(geo_df['Strain'] == s)]['colour'].tolist() 136 </div>
137 myPal.append(col[0]) 137
138 print(myPal) 138 <div class="d-flex flex-items-center">
139 mycogmap = ['skyblue', 'orangered'] # blue absent,red present 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="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;99EA:03C4:48319:89CA2:5CF56242&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_V.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="2b5b3e285e06f6291d9585d00d3c451a25d337d3be9971ebaefb9cb398fb4ecc" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
140 tv_df.set_index('COG', inplace=True) 140 Sign&nbsp;up
141 tv_df = tv_df[tv_df.columns].astype(float) 141 </a>
142 142 <button class="btn-link d-lg-none mt-1 js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
143 cg = sns.clustermap(tv_df, method='ward', col_colors=myPal, cmap=mycogmap, yticklabels = 1500, row_cluster=False, linewidths = 0) 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>
144 #cg = sns.clustermap(tv_df, method='ward', row_cluster=False, linewidths = 0) 144 </button>
145 ax = cg.ax_heatmap 145 </div>
146 #xasix ticks and labels. 146 </div>
147 ax.xaxis.tick_top() #set ticks at top 147
148 newlabs = [] 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">
149 149 <div class="d-flex d-lg-none flex-justify-end border-bottom bg-gray-light p-3">
150 labs = ax.xaxis.get_ticklabels() 150 <button class="btn-link js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
151 for i in range(0, len(labs)): 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>
152 print(labs[i]) 152 </button>
153 # labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars 153 </div>
154 newlabs.append(" " + labs[i].get_text()) 154
155 ax.xaxis.set_ticklabels(newlabs) 155 <nav class="mt-0 px-3 px-lg-0 mb-5 mb-lg-0" aria-label="Global">
156 156 <ul class="d-lg-flex list-style-none">
157 #labs = ax.xaxis.get_ticklabels() 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 ">
158 #for i in range(0, len(labs)): 158 <details class="HeaderMenu-details details-overlay details-reset width-full">
159 # print(labs[i]) 159 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
160 # labs[i].set_text(" "+labs[i].get_text()) #make enough room so label sits atop of col_color bars 160 Why GitHub?
161 # print(labs[i]) 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">
162 #ax.xaxis.set_ticklabels(labs) 162 <path d="M1,1l6.2,6L13,1"></path>
163 plt.setp(cg.ax_heatmap.xaxis.get_ticklabels(), rotation=90) # get x labels printed vertically 163 </svg>
164 164 </summary>
165 cg.cax.set_visible(False) 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">
166 ax = cg.ax_heatmap 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">&rarr;</span></a>
167 ax.set_yticklabels("") 167 <ul class="list-style-none f5 pb-3">
168 ax.set_ylabel("") 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>
169 ax = cg.ax_heatmap 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>
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") 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>
171 b = len(tv_df) 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>
172 print(b) 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>
173 title = "Figure Legend: The Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ " \ 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>
174 "showing the \ncombination of present and absent diagnostic cluster of VSG orthologs " \ 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>
175 "across the sample cohort. \nDendrogram reflects the relationships amongst the VSG" \ 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>
176 " repertoires of each strain. " \ 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>
177 "Strains were isolated \nfrom multiple African countries as shown in the key.\nData was produced with the " \ 177 </ul>
178 "'Variant Antigen Profiler' (Silva Pereira and Jackson, 2018)." 178
179 179 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
180 ax.text(-1.5, len(tv_df) + 8, 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">&rarr;</span></a></li>
181 title, 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">&rarr;</span></a></li>
182 ha="left", va="top", wrap="True") 182 </ul>
183 col = cg.ax_col_dendrogram.get_position() 183 </div>
184 cg.ax_col_dendrogram.set_position([col.x0, col.y0*1.08, col.width, col.height*1.1]) 184 </details>
185 185 </li>
186 countryList = pd.unique(geo_df['Location']) 186 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
187 colourList = pd.unique(geo_df['colour']) 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>
188 legend_elements = [Patch(facecolor='orangered', label='COG Present'), 188 </li>
189 Patch(facecolor='skyblue', label='COG Absent')] 189
190 190 <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 ">
191 for i in range(0, len(colourList)): 191 <details class="HeaderMenu-details details-overlay details-reset width-full">
192 print("country = %s, colour = %s" % (countryList[i], colourList[i])) 192 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
193 p = Patch(facecolor=str(colourList[i]), label=countryList[i]) 193 Explore
194 legend_elements.append(p) 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">
195 195 <path d="M1,1l6.2,6L13,1"></path>
196 ax.legend(handles = legend_elements, bbox_to_anchor=(-0.3,1.2),loc = 'upper left') 196 </svg>
197 197 </summary>
198 198
199 199 <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">
200 200 <ul class="list-style-none mb-3">
201 201 <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">&rarr;</span></a></li>
202 202 </ul>
203 203
204 #plt.setp(cg.ax_heatmap.yaxis.get_ticklabels(), rotation=0 ) # get y labels printed horizontally 204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn &amp; contribute</h4>
205 # cg.dendrogram_col.linkage # linkage matrix for columns 205 <ul class="list-style-none mb-3">
206 # cg.dendrogram_row.linkage # linkage matrix for rows 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>
207 # plt.savefig(r"results/" + name + "_heatmap.png") 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>
208 #plt.savefig(htmlresource + "/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>
209 #if pdf == 'PDF_Yes': 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>
210 # plt.savefig(htmlresource + "/heatmap.pdf") 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>
211 # shutil.copyfile("heatmap.pdf",heatmapfn) # 211 </ul>
212 #plt.legend() 212
213 fname = html_path+"/"+name+"_clustermap.png" 213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4>
214 cg.savefig(fname) 214 <ul class="list-style-none mb-0">
215 if pdfExport == 'PDF_Yes': 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>
216 fname = html_path + "/" + name + "_clustermap.pdf" 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>
217 cg.savefig(fname) 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>
218 #plt.show() 218 </ul>
219 219 </div>
220 def createHTML(name,htmlfn,htmlPath): 220 </details>
221 #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource 221 </li>
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>" 222
223 htmlString += name 223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
224 224 <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>
225 225 </li>
226 htmlString += r'<p> <h3>The Heat Map and Dendrogram</h3></p>' 226
227 imgString = r"<img src = '"+name+"_clustermap.png' alt='Cog Clustermap' style='max-width:100%'><br><br>" 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 ">
228 htmlString += imgString 228 <details class="HeaderMenu-details details-overlay details-reset width-full">
229 print(htmlString) 229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
230 230 Pricing
231 with open(htmlfn, "w") as htmlfile: 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">
232 htmlfile.write(htmlString) 232 <path d="M1,1l6.2,6L13,1"></path>
233 233 </svg>
234 234 </summary>
235 def vivax_assemble(args,dict): 235
236 #argdict = {'name': 2, 'pdfexport': 3, 'kmers': 4, 'inslen': 5, 'covcut': 6, 'forward': 7, 'reverse': 8, 'html_file': 9,'html_resource': 10} 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">
237 #assembleWithVelvet("V2_Test", '65', '400', '5', "data/TviBrRp.1.clean", "data/TviBrRp.2.clean") 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">&rarr;</span></a>
238 238
239 vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax" 239 <ul class="list-style-none mb-3">
240 assembleWithVelvet(args[dict['name']], args[dict['kmers']], args[dict['inslen']], args[dict['covcut']], 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>
241 args[dict['forward']], args[dict['reverse']]) 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>
242 blastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/COGs.fas") 242 </ul>
243 orthPresence_df = getCogsPresent(blastResult_df, args[dict['name']], vivaxPath+r"/Database/COGlist.txt") 243
244 244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
245 binBlastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/Bin_2.fas") 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">&rarr;</span></a></li>
246 binPresence_df = getCogsPresent(binBlastResult_df, args[dict['name']], vivaxPath+r"/Database/binlist.txt") 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">&rarr;</span></a></li>
247 cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True) 247 </ul>
248 248 </div>
249 fname = args[dict['html_resource']] +args[dict['name']]+"_cogspresent.csv" 249 </details>
250 cogPresence_df.to_csv(fname) 250 </li>
251 current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. 251 </ul>
252 createClusterMap(current_df, args[dict['name']],args[dict['html_resource']],args[dict['pdfexport']]) 252 </nav>
253 createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']]) 253
254 254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left">
255 def test_cluster(args,dict): 255 <div class="d-lg-flex mb-3 mb-lg-0">
256 print ("name: %s",args[dict['name']]) 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"
257 cogPresence_df = pd.read_csv("test_cogspresent.csv") 257 role="combobox"
258 print(cogPresence_df) 258 aria-owns="jump-to-results"
259 current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. 259 aria-label="Search or jump to"
260 createClusterMap(current_df, args[dict['name']], args[dict['html_resource']], args[dict['pdfexport']]) 260 aria-haspopup="listbox"
261 261 aria-expanded="false"
262 def vivax_contigs(args,dict): 262 >
263 # argdict = {'name': 2, 'pdfexport': 3, 'contigs': 4, 'html_file': 5, 'html_resource': 6} 263 <div class="position-relative">
264 264 <!-- '"` --><!-- </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="&#x2713;" />
265 #test_cluster(args,dict) 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">
266 #return; 266 <input type="text"
267 267 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"
268 #subprocess.call('echo $PATH',shell = True) 268 data-hotkey="s,/"
269 #sys.exit(1) 269 name="q"
270 270 value=""
271 vivaxPath = os.path.dirname(os.path.realpath(__file__))+r"/data/vivax" 271 placeholder="Search"
272 shutil.copyfile(args[dict['contigs']], args[dict['name']]+".fa") 272 data-unscoped-placeholder="Search GitHub"
273 blastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/COGs.fas") 273 data-scoped-placeholder="Search"
274 orthPresence_df = getCogsPresent(blastResult_df, args[dict['name']], vivaxPath+r"/Database/COGlist.txt") 274 autocapitalize="off"
275 275 aria-autocomplete="list"
276 binBlastResult_df = blastContigs(args[dict['name']], vivaxPath+r"/Database/Bin_2.fas") 276 aria-controls="jump-to-results"
277 binPresence_df = getCogsPresent(binBlastResult_df, args[dict['name']], vivaxPath+r"/Database/binlist.txt") 277 aria-label="Search"
278 cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True) 278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=UBI6zrTC3YpC0k8lrlu6srLfkSoG1pT6oQPtlColDmhV/VRup2DMPG2/7aV0Ny9S/lUPp8loX+6gx+nMJGy0Tg=="
279 279 spellcheck="false"
280 fname = args[dict['html_resource']]+r"/"+ args[dict['name']]+"_cogspresent.csv" 280 autocomplete="off"
281 cogPresence_df.to_csv(fname) 281 >
282 current_df = addToCurrentData(cogPresence_df,args[dict['name']]) # load in Tvdatabase and add cogPresence column to it. 282 <input type="hidden" class="js-site-search-type-field" name="type" >
283 createClusterMap(current_df, args[dict['name']], args[dict['html_resource']], args[dict['pdfexport']]) 283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
284 createHTML(args[dict['name']],args[dict['html_file']],args[dict['html_resource']]) 284
285 285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
286 if __name__ == "__main__": 286
287 #assembleWithVelvet("V2_Test",'65','400', '5',"data/TviBrRp.1.clean","data/TviBrRp.2.clean") 287 <ul class="d-none js-jump-to-suggestions-template-container">
288 #assembleWithVelvet("V2_Test",'65','400', '5',"data/Tv493.1","data/Tv493.2") 288
289 #blastResult_df=blastContigs("V2_Test",r"/Database/COGs.fas") 289
290 cogPresence_df = pd.read_csv("test_cogspresent.csv") 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">
291 print(cogPresence_df) 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="">
292 current_df = addToCurrentData(cogPresence_df,"vTest") # load in Tvdatabase and add cogPresence column to it. 292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
293 createClusterMap(current_df, "vTest", "sausages","no") 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 createHTML("vTest","vTest.html","sausages") 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 sys.exit() 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>
296 296 </div>
297 blastResult_df=blastContigs("Tv493",r"/Database/COGs.fas") 297
298 orthPresence_df = getCogsPresent(blastResult_df,"Tv493",r"/Database/COGlist.txt") 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">
299 299
300 #binBlastResult_df=blastContigs("V2_Test",r"/Database/Bin_2.fas") 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">
301 301 </div>
302 binBlastResult_df=blastContigs("Tv493",r"/Database/Bin_2.fas") 302
303 binPresence_df = getCogsPresent(binBlastResult_df,"Tv493",r"/Database/binlist.txt") 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 cogPresence_df = orthPresence_df.append(binPresence_df, ignore_index=True) 304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
305 #now do the next bit? 305 In this repository
306 current_df = addToCurrentData(cogPresence_df) # load in Tvdatabase and add cogPresence column to it. 306 </span>
307 createClusterMap(current_df,'Test',dict['html_resource'] ,dict['pdfexport']) 307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
308 308 All GitHub
309 309 </span>
310 #print(cogPresence_df) 310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
311 dir_path = os.path.dirname(os.path.realpath(__file__)) 311 </div>
312 fname = dir_path+r"/results/V2_TestPresence.csv" 312
313 #fnameb = dir_path+r"/results/V2_Test_blastOrth.csv" 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 #fnameb_bin = dir_path+r"/results/V2_Test_blastBin.csv" 314 Jump to
315 #binBlastResult_df.to_csv(fnameb_bin) 315 <span class="d-inline-block ml-1 v-align-middle">↵</span>
316 #blastResult_df.to_csv(fnameb) 316 </div>
317 317 </a>
318 #cogPresence_df.to_csv(fname) 318 </li>
319 cogPresence_df = pd.read_csv(fname) 319
320 320 </ul>
321 current_df = addToCurrentData(cogPresence_df) #load in Tvdatabase and add cogPresence column to it. 321
322 322 <ul class="d-none js-jump-to-no-results-template-container">
323 323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2">
324 324 <span class="text-gray">No suggested jump to results</span>
325 325 </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">
334 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
335 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
336 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
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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">&quot;&quot;&quot;</span></span></td>
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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>
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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>
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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 &quot;License&quot;);</span></td>
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750 </tr>
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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>
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770 </tr>
771 <tr>
772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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774 </tr>
775 <tr>
776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
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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">&quot;&quot;&quot;</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">&#39;</span>Agg<span class="pl-pds">&#39;</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 = &quot;velveth &quot; + name + &quot;_k65 65 -shortPaired -fastq &quot; + name + &quot;_R1.fastq &quot; + name + &quot;_R2.fastq&quot;</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">&quot;</span>velveth <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> kmers <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span> -shortPaired -fastq <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> fastq1name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> <span class="pl-pds">&quot;</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">&quot;</span>Error in velveth<span class="pl-pds">&quot;</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">&quot;</span>velvetg <span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -exp_cov auto -ins_length <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inslen<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -clean yes -ins_length_sd 50 -min_pair_count 20<span class="pl-pds">&quot;</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 = &quot;velvetg &quot; + name + &quot;_k&quot;+kmers+&quot; -exp_cov auto -ins_length &quot;+inslen+&quot; -cov_cutoff &quot;+covcut+&quot; -clean yes -ins_length_sd 50 -min_pair_count 20&quot;</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 = &quot;velvetg &quot; + name + &quot;_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20&quot;+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">&quot;</span>Error in velvetg<span class="pl-pds">&quot;</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">&quot;</span>_k<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>kmers<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>//contigs.fa<span class="pl-pds">&quot;</span></span>,name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.fa<span class="pl-pds">&quot;</span></span>) <span class="pl-c"><span class="pl-c">#</span> my $namechange = &quot;mv &quot;.$input.&quot;_k65/contigs.fa &quot;.$input.&quot;.fa&quot;;</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">&quot;</span>ok<span class="pl-pds">&quot;</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">&quot;</span>blastn -db <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -query <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.fa -outfmt 10 -out <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_blast.txt<span class="pl-pds">&quot;</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">&quot;</span>Error in blastall<span class="pl-pds">&quot;</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">&quot;</span><span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_blast.txt<span class="pl-pds">&quot;</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] &gt;= 98 &amp; &amp; $temp[3] &gt; 100 &amp; &amp; $temp[10] &lt; 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>&#39;qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore&#39;</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">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>length<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>mismatch<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>gapopen<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>qstart<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>qend<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>sstart<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>send<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>bitscore<span class="pl-pds">&#39;</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">&#39;</span>pident<span class="pl-pds">&#39;</span></span>]<span class="pl-k">&gt;=</span><span class="pl-c1">98</span>) <span class="pl-k">&amp;</span> (blast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>length<span class="pl-pds">&#39;</span></span>] <span class="pl-k">&gt;</span> <span class="pl-c1">100</span>) <span class="pl-k">&amp;</span> (blast_df[<span class="pl-s"><span class="pl-pds">&#39;</span>evalue<span class="pl-pds">&#39;</span></span>]<span class="pl-k">&lt;</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">&#39;</span>qaccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>saccver<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pident<span class="pl-pds">&#39;</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">&#39;</span>pident<span class="pl-pds">&#39;</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">&#39;</span>qaccver<span class="pl-pds">&#39;</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">&#39;</span>saccver<span class="pl-pds">&#39;</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">&#39;</span><span class="pl-cce">\n\r</span> <span class="pl-pds">&#39;</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">&#39;</span><span class="pl-cce">\n\r</span> <span class="pl-pds">&#39;</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">&#39;</span>1<span class="pl-pds">&#39;</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">&#39;</span>0<span class="pl-pds">&#39;</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">&#39;</span>Cog<span class="pl-pds">&#39;</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">&quot;</span>/data/vivax/TvDatabase<span class="pl-c1">.</span>csv<span class="pl-pds">&quot;</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,&#39;Test&#39;)</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">&quot;</span>/data/vivax/geoTv<span class="pl-c1">.</span>csv<span class="pl-pds">&quot;</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">&#39;</span>k<span class="pl-pds">&#39;</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">&#39;</span>Strain<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> s)][<span class="pl-s"><span class="pl-pds">&#39;</span>colour<span class="pl-pds">&#39;</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">&#39;</span>skyblue<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>orangered<span class="pl-pds">&#39;</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">&#39;</span>COG<span class="pl-pds">&#39;</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">&#39;</span>ward<span class="pl-pds">&#39;</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=&#39;ward&#39;, 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(&quot; &quot;+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">&quot;</span> <span class="pl-pds">&quot;</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(&quot; &quot;+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">&quot;</span><span class="pl-pds">&quot;</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">&quot;</span><span class="pl-pds">&quot;</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(&quot;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.&quot;, va = &quot;top&quot;, wrap = &quot;True&quot;)</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">&quot;</span>Figure Legend: The Variant Antigen Profiles of $\itTrypanosoma$ $\itvivax$ <span class="pl-pds">&quot;</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">&quot;</span>showing the <span class="pl-cce">\n</span>combination of present and absent diagnostic cluster of VSG orthologs <span class="pl-pds">&quot;</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">&quot;</span>across the sample cohort. <span class="pl-cce">\n</span>Dendrogram reflects the relationships amongst the VSG<span class="pl-pds">&quot;</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">&quot;</span> repertoires of each strain. <span class="pl-pds">&quot;</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">&quot;</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">&quot;</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">&quot;</span>&#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</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">&quot;</span>left<span class="pl-pds">&quot;</span></span>, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>top<span class="pl-pds">&quot;</span></span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>True<span class="pl-pds">&quot;</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">&#39;</span>Location<span class="pl-pds">&#39;</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">&#39;</span>colour<span class="pl-pds">&#39;</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">&#39;</span>orangered<span class="pl-pds">&#39;</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>COG Present<span class="pl-pds">&#39;</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">&#39;</span>skyblue<span class="pl-pds">&#39;</span></span>, <span class="pl-v">label</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>COG Absent<span class="pl-pds">&#39;</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">&quot;</span>country = <span class="pl-c1">%s</span>, colour = <span class="pl-c1">%s</span><span class="pl-pds">&quot;</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">&#39;</span>upper left<span class="pl-pds">&#39;</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&quot;results/&quot; + name + &quot;_heatmap.png&quot;)</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 + &quot;/heatmap.png&quot;)</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 == &#39;PDF_Yes&#39;:</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 + &quot;/heatmap.pdf&quot;)</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(&quot;heatmap.pdf&quot;,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">&quot;</span>/<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_clustermap.png<span class="pl-pds">&quot;</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">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</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">&quot;</span>/<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>_clustermap.pdf<span class="pl-pds">&quot;</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">&quot;</span>&lt;html&gt;&lt;title&gt;T<span class="pl-c1">.</span>vivax VAP&lt;/title&gt;&lt;body&gt;&lt;div style=&#39;text-align:center&#39;&gt;&lt;h2&gt;&lt;i&gt;Trypanosoma vivax&lt;/i&gt; Variant Antigen Profile&lt;/h2&gt;&lt;h3&gt;<span class="pl-pds">&quot;</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">&#39;</span>&lt;p&gt; &lt;h3&gt;The Heat Map and Dendrogram&lt;/h3&gt;&lt;/p&gt;<span class="pl-pds">&#39;</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">&quot;</span>&lt;img src = &#39;<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_clustermap.png&#39; alt=&#39;Cog Clustermap&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</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">&quot;</span>w<span class="pl-pds">&quot;</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 = {&#39;name&#39;: 2, &#39;pdfexport&#39;: 3, &#39;kmers&#39;: 4, &#39;inslen&#39;: 5, &#39;covcut&#39;: 6, &#39;forward&#39;: 7, &#39;reverse&#39;: 8, &#39;html_file&#39;: 9,&#39;html_resource&#39;: 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(&quot;V2_Test&quot;, &#39;65&#39;, &#39;400&#39;, &#39;5&#39;, &quot;data/TviBrRp.1.clean&quot;, &quot;data/TviBrRp.2.clean&quot;)</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">&quot;</span>/data/vivax<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>kmers<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>inslen<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>covcut<span class="pl-pds">&#39;</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">&#39;</span>forward<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">&quot;</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">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]] <span class="pl-k">+</span>args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_cogspresent.csv<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</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">&quot;</span>name: <span class="pl-c1">%s</span><span class="pl-pds">&quot;</span></span>,args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</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">&quot;</span>test_cogspresent.csv<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</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 = {&#39;name&#39;: 2, &#39;pdfexport&#39;: 3, &#39;contigs&#39;: 4, &#39;html_file&#39;: 5, &#39;html_resource&#39;: 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(&#39;echo $PATH&#39;,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">&quot;</span>/data/vivax<span class="pl-pds">&quot;</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">&#39;</span>contigs<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.fa<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/COGs<span class="pl-c1">.</span>fas<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/COGlist<span class="pl-c1">.</span>txt<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/Bin_2<span class="pl-c1">.</span>fas<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], vivaxPath<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/Database/binlist<span class="pl-c1">.</span>txt<span class="pl-pds">&quot;</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">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span> args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_cogspresent.csv<span class="pl-pds">&quot;</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">&#39;</span>name<span class="pl-pds">&#39;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]], args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</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">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</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">&quot;</span>__main__<span class="pl-pds">&quot;</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>
1931 <tr>
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>
1935 </tr>
1936 <tr>
1937 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
1938 <td id="LC291" class="blob-code blob-code-inner js-file-line">
1939 </td>
1940 </tr>
1941 <tr>
1942 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
1943 <td id="LC292" class="blob-code blob-code-inner js-file-line">
1944 </td>
1945 </tr>
1946 </table>
1947
1948 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
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