annotate Tryp_T.py @ 13:8c210b4ad003 draft

Uploaded
author johnheap
date Mon, 03 Jun 2019 14:29:04 -0400
parents 25226d33642e
children 5e346d75ccf3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
3
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
4
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
5
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
6
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
7 <!DOCTYPE html>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
8 <html lang="en">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
9 <head>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
10 <meta charset="utf-8">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
11 <link rel="dns-prefetch" href="https://github.githubassets.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
18
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
19
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
20
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
21 <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
22 <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
24
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
25
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
26
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
27
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
28
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
29 <meta name="viewport" content="width=device-width">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
30
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
31 <title>VAPPER-Galaxy/Tryp_T.py at master · johnheap/VAPPER-Galaxy · GitHub</title>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
32 <meta name="description" content="Contribute to johnheap/VAPPER-Galaxy development by creating an account on GitHub.">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
33 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
34 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
35 <meta property="fb:app_id" content="1401488693436528">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
36
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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." />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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." />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
39
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
40 <link rel="assets" href="https://github.githubassets.com/">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
41
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
42 <meta name="pjax-timeout" content="1000">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
43
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
44 <meta name="request-id" content="A68B:03C7:99543:10DBF9:5CF561B6" data-pjax-transient>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
45
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
46
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
47
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
48
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
49 <meta name="selected-link" value="repo_source" data-pjax-transient>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
50
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
51 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
52 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
53 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
54
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
55 <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="A68B:03C7:99543:10DBF9:5CF561B6" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
56 <meta name="analytics-location" content="/&lt;user-name&gt;/&lt;repo-name&gt;/blob/show" data-pjax-transient="true" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
57
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
58
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
59
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
60 <meta name="google-analytics" content="UA-3769691-2">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
61
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
62
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
63 <meta class="js-ga-set" name="dimension1" content="Logged Out">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
64
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
65
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
66
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
67
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
68
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
69 <meta name="hostname" content="github.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
70 <meta name="user-login" content="">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
71
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
72 <meta name="expected-hostname" content="github.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
73 <meta name="js-proxy-site-detection-payload" content="MzM5YjY3ZjNjYzY5Y2RhNDI5MDYxM2MzZTc0ZGExYzUxM2I3NjhiNTdmNGE2NjMwYWVjMzFhMGIzNWY0MDU3OHx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiJBNjhCOjAzQzc6OTk1NDM6MTBEQkY5OjVDRjU2MUI2IiwidGltZXN0YW1wIjoxNTU5NTg1MjA3LCJob3N0IjoiZ2l0aHViLmNvbSJ9">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
74
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
75 <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
76
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
77 <meta name="html-safe-nonce" content="632a90d8ff46863b6a26a12d9d6ed92a6679abbf">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
78
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
79 <meta http-equiv="x-pjax-version" content="af1499c2254d0582d0a98af1dfd7f11b">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
80
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
81
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
83
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
84 <meta name="go-import" content="github.com/johnheap/VAPPER-Galaxy git https://github.com/johnheap/VAPPER-Galaxy.git">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
85
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
87
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
88
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
89 <link rel="canonical" href="https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py" data-pjax-transient>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
90
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
91
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
92 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
93
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
94 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
95
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
96 <link rel="mask-icon" href="https://github.githubassets.com/pinned-octocat.svg" color="#000000">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
97 <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://github.githubassets.com/favicon.ico">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
98
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
99 <meta name="theme-color" content="#1e2327">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
100
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
101
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
102
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
103
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
104
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
105 <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
106
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
107 </head>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
108
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
109 <body class="logged-out env-production page-responsive page-blob">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
110
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
111
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
112 <div class="position-relative js-header-wrapper ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
114 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
115
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
116
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
117
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
118
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
119
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
120
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
121 <header class="Header-old header-logged-out js-details-container Details position-relative f4 py-2" role="banner">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
122 <div class="container-lg d-lg-flex flex-items-center p-responsive">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
123 <div class="d-flex flex-justify-between flex-items-center">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
124 <a class="mr-4" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
126 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
127
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
128 <div class="d-lg-none css-truncate css-truncate-target width-fit p-2">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
129
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
131 <a class="Header-link" href="/johnheap">johnheap</a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
132 /
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
133 <a class="Header-link" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
134
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
135
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
136 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
137
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
138 <div class="d-flex flex-items-center">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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;A68B:03C7:99543:10DBF9:5CF561B6&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="2815673fe800ea60b3399372453cd6ad235f12180cead78fa9534b2f8d8e77a5" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
140 Sign&nbsp;up
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
141 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
142 <button class="btn-link d-lg-none mt-1 js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
144 </button>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
145 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
146 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
147
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
149 <div class="d-flex d-lg-none flex-justify-end border-bottom bg-gray-light p-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
150 <button class="btn-link js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
152 </button>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
153 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
154
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
155 <nav class="mt-0 px-3 px-lg-0 mb-5 mb-lg-0" aria-label="Global">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
156 <ul class="d-lg-flex list-style-none">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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 ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
158 <details class="HeaderMenu-details details-overlay details-reset width-full">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
159 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
160 Why GitHub?
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
162 <path d="M1,1l6.2,6L13,1"></path>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
163 </svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
164 </summary>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
167 <ul class="list-style-none f5 pb-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
177 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
178
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
179 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
182 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
183 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
184 </details>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
185 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
186 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
188 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
189
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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 ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
191 <details class="HeaderMenu-details details-overlay details-reset width-full">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
192 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
193 Explore
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
195 <path d="M1,1l6.2,6L13,1"></path>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
196 </svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
197 </summary>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
198
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
200 <ul class="list-style-none mb-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
202 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
203
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
204 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn &amp; contribute</h4>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
205 <ul class="list-style-none mb-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
211 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
212
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
213 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
214 <ul class="list-style-none mb-0">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
218 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
219 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
220 </details>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
221 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
222
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
223 <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
225 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
226
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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 ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
228 <details class="HeaderMenu-details details-overlay details-reset width-full">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
229 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
230 Pricing
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
232 <path d="M1,1l6.2,6L13,1"></path>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
233 </svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
234 </summary>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
235
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
238
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
239 <ul class="list-style-none mb-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
242 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
243
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
244 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
247 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
248 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
249 </details>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
250 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
251 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
252 </nav>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
253
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
254 <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
255 <div class="d-lg-flex mb-3 mb-lg-0">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
257 role="combobox"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
258 aria-owns="jump-to-results"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
259 aria-label="Search or jump to"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
260 aria-haspopup="listbox"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
261 aria-expanded="false"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
262 >
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
263 <div class="position-relative">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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;" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
266 <input type="text"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
268 data-hotkey="s,/"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
269 name="q"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
270 value=""
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
271 placeholder="Search"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
272 data-unscoped-placeholder="Search GitHub"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
273 data-scoped-placeholder="Search"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
274 autocapitalize="off"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
275 aria-autocomplete="list"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
276 aria-controls="jump-to-results"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
277 aria-label="Search"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
278 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=aIF6VlsMjmBGKiH9gFW0N7Dd6tKGBfaVG4YIMScDT9WHVDbYUTh6gnqmb9yMT8saP+1TzsRaVWx++i39m514Bw=="
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
279 spellcheck="false"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
280 autocomplete="off"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
281 >
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
282 <input type="hidden" class="js-site-search-type-field" name="type" >
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
283 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
284
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
285 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
286
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
287 <ul class="d-none js-jump-to-suggestions-template-container">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
288
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
289
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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="">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
292 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
296 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
297
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
299
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
301 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
302
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
304 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
305 In this repository
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
306 </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
307 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
308 All GitHub
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
309 </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
310 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
311 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
312
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
314 Jump to
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
315 <span class="d-inline-block ml-1 v-align-middle">↵</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
316 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
317 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
318 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
319
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
320 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
321
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
322 <ul class="d-none js-jump-to-no-results-template-container">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
323 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
324 <span class="text-gray">No suggested jump to results</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
325 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
326 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
327
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
329
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
330
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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="">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
333 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
337 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
338
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
339 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
340
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
341 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
342 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
343
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
344 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
345 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
346 In this repository
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
347 </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
348 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
349 All GitHub
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
350 </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
351 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
352 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
353
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
354 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
355 Jump to
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
356 <span class="d-inline-block ml-1 v-align-middle">↵</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
357 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
358 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
359 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
360
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
361
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
362
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
363 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
364 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
365 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
366 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
367 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
368 <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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
369 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
370
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
371 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
372
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
373 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
374 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
375
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
376 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
377 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
378 In this repository
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
379 </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
380 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
381 All GitHub
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
382 </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
383 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
384 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
385
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
386 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
387 Jump to
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
388 <span class="d-inline-block ml-1 v-align-middle">↵</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
389 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
390 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
391 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
392
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
393
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
394 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
395
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
396 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
397 </label>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
398 </form> </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
399 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
400
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
401 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
402
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
403 <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A68B:03C7:99543:10DBF9:5CF561B6&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="ee13ebea83318ac27e6a65b780a208b4ce93890e3887689f786a3a86a3aa41cb" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy%2Fblob%2Fmaster%2FTryp_T.py">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
404 Sign&nbsp;in
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
405 </a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&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;A68B:03C7:99543:10DBF9:5CF561B6&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="ff072ec41895d40692c4e40554c544f4e6d3a197b0aa2bc35ed34ef5987a3ec2" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join?source=header-repo">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
406 Sign&nbsp;up
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
407 </a> </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
408 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
409 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
410 </header>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
411
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
412 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
413
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
414 <div id="start-of-content" class="show-on-focus"></div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
415
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
416
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
417 <div id="js-flash-container">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
418
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
419 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
420
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
421
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
422
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
423 <div class="application-main " data-commit-hovercards-enabled>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
424 <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class="">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
425 <main >
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
426
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
427
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
428
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
429
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
430
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
431
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
432
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
433
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
434
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
435
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
436 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav pt-0 pt-lg-4 ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
437 <div class="repohead-details-container clearfix container-lg p-responsive d-none d-lg-block">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
438
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
439 <ul class="pagehead-actions">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
440
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
441
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
442
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
443
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
444 <li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
445
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
446 <a class="tooltipped tooltipped-s btn btn-sm btn-with-count" aria-label="You must be signed in to watch a repository" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;notification subscription menu watch&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A68B:03C7:99543:10DBF9:5CF561B6&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="303fe83d7f28189cc1006654f2b9fbccd2c8838444327b8f33c609f157702b21" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
447 <svg class="octicon octicon-eye v-align-text-bottom" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
448 Watch
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
449 </a> <a class="social-count" href="/johnheap/VAPPER-Galaxy/watchers"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
450 aria-label="0 users are watching this repository">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
451 0
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
452 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
453
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
454 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
455
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
456 <li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
457 <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to star a repository" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;star button&quot;,&quot;repository_id&quot;:139730674,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A68B:03C7:99543:10DBF9:5CF561B6&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="0b7f28f0aecc977595e6f55f43272a0e1be4f4f7700f4f26ab93eae1b5fa8ee1" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
458 <svg class="octicon octicon-star v-align-text-bottom" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74L14 6z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
459 Star
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
460 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
461 <a class="social-count js-social-count" href="/johnheap/VAPPER-Galaxy/stargazers"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
462 aria-label="0 users starred this repository">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
463 0
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
464 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
465
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
466 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
467
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
468 <li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
469 <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to fork a repository" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;repo details fork button&quot;,&quot;repository_id&quot;:139730674,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;A68B:03C7:99543:10DBF9:5CF561B6&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="cb93cd40277ba7752d7d1cb24a212cbd8c94065f1bb5f20aa10db6bb11698ef0" href="/login?return_to=%2Fjohnheap%2FVAPPER-Galaxy">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
470 <svg class="octicon octicon-repo-forked v-align-text-bottom" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
471 Fork
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
472 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
473 <a href="/johnheap/VAPPER-Galaxy/network/members" class="social-count"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
474 aria-label="0 users forked this repository">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
475 0
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
476 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
477 </li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
478 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
479
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
480 <h1 class="public ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
481 <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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
482 <span class="author" itemprop="author"><a class="url fn" rel="author" data-hovercard-type="user" data-hovercard-url="/hovercards?user_id=24318980" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/johnheap">johnheap</a></span><!--
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
483 --><span class="path-divider">/</span><!--
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
484 --><strong itemprop="name"><a data-pjax="#js-repo-pjax-container" href="/johnheap/VAPPER-Galaxy">VAPPER-Galaxy</a></strong>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
485
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
486
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
487 </h1>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
488
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
489 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
490
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
491 <nav class="hx_reponav reponav js-repo-nav js-sidenav-container-pjax container-lg p-responsive d-none d-lg-block"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
492 itemscope
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
493 itemtype="http://schema.org/BreadcrumbList"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
494 aria-label="Repository"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
495 data-pjax="#js-repo-pjax-container">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
496
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
497 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
498 <a class="js-selected-navigation-item selected reponav-item" itemprop="url" data-hotkey="g c" aria-current="page" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /johnheap/VAPPER-Galaxy" href="/johnheap/VAPPER-Galaxy">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
499 <svg class="octicon octicon-code" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M9.5 3L8 4.5 11.5 8 8 11.5 9.5 13 14 8 9.5 3zm-5 0L0 8l4.5 5L6 11.5 2.5 8 6 4.5 4.5 3z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
500 <span itemprop="name">Code</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
501 <meta itemprop="position" content="1">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
502 </a> </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
503
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
504 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
505 <a itemprop="url" data-hotkey="g i" class="js-selected-navigation-item reponav-item" data-selected-links="repo_issues repo_labels repo_milestones /johnheap/VAPPER-Galaxy/issues" href="/johnheap/VAPPER-Galaxy/issues">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
506 <svg class="octicon octicon-issue-opened" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
507 <span itemprop="name">Issues</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
508 <span class="Counter">0</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
509 <meta itemprop="position" content="2">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
510 </a> </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
511
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
512 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
513 <a data-hotkey="g p" itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /johnheap/VAPPER-Galaxy/pulls" href="/johnheap/VAPPER-Galaxy/pulls">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
514 <svg class="octicon octicon-git-pull-request" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
515 <span itemprop="name">Pull requests</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
516 <span class="Counter">0</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
517 <meta itemprop="position" content="3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
518 </a> </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
519
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
520
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
521 <a data-hotkey="g b" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /johnheap/VAPPER-Galaxy/projects" href="/johnheap/VAPPER-Galaxy/projects">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
522 <svg class="octicon octicon-project" viewBox="0 0 15 16" version="1.1" width="15" height="16" aria-hidden="true"><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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
523 Projects
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
524 <span class="Counter" >0</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
525 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
526
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
527
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
528 <a data-skip-pjax="true" class="js-selected-navigation-item reponav-item" data-selected-links="security alerts policy /johnheap/VAPPER-Galaxy/security/advisories" href="/johnheap/VAPPER-Galaxy/security/advisories">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
529 <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" class="octicon" height="16px" width="16px">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
530 <path fill-rule="evenodd" clip-rule="evenodd" d="M1 2l7-2 7 2v6.02C15 12.69 9.69 16 8 16c-1.69 0-7-3.31-7-7.98V2zm1 .75L8 1l6 1.75v5.268C14 12.104 9.45 15 8 15c-1.45 0-6-2.896-6-6.982V2.75z"></path>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
531 <path d="M3 3.5L8 2v12c-1.207 0-5-2.482-5-5.985V3.5z"></path>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
532 </svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
533
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
534 Security
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
535 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
536 <a class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors dependency_graph pulse people /johnheap/VAPPER-Galaxy/pulse" href="/johnheap/VAPPER-Galaxy/pulse">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
537 <svg class="octicon octicon-graph" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
538 Insights
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
539 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
540
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
541 </nav>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
542
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
543 <div class="reponav-wrapper reponav-small d-lg-none">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
544 <nav class="reponav js-reponav text-center no-wrap"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
545 itemscope
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
546 itemtype="http://schema.org/BreadcrumbList">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
547
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
548 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
549 <a class="js-selected-navigation-item selected reponav-item" itemprop="url" aria-current="page" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /johnheap/VAPPER-Galaxy" href="/johnheap/VAPPER-Galaxy">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
550 <span itemprop="name">Code</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
551 <meta itemprop="position" content="1">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
552 </a> </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
553
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
554 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
555 <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_issues repo_labels repo_milestones /johnheap/VAPPER-Galaxy/issues" href="/johnheap/VAPPER-Galaxy/issues">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
556 <span itemprop="name">Issues</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
557 <span class="Counter">0</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
558 <meta itemprop="position" content="2">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
559 </a> </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
560
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
561 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
562 <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /johnheap/VAPPER-Galaxy/pulls" href="/johnheap/VAPPER-Galaxy/pulls">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
563 <span itemprop="name">Pull requests</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
564 <span class="Counter">0</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
565 <meta itemprop="position" content="3">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
566 </a> </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
567
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
568 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
569 <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /johnheap/VAPPER-Galaxy/projects" href="/johnheap/VAPPER-Galaxy/projects">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
570 <span itemprop="name">Projects</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
571 <span class="Counter">0</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
572 <meta itemprop="position" content="4">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
573 </a> </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
574
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
575
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
576 <a itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="security alerts policy /johnheap/VAPPER-Galaxy/security/advisories" href="/johnheap/VAPPER-Galaxy/security/advisories">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
577 <span itemprop="name">Security</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
578 <meta itemprop="position" content="6">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
579 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
580 <a class="js-selected-navigation-item reponav-item" data-selected-links="pulse /johnheap/VAPPER-Galaxy/pulse" href="/johnheap/VAPPER-Galaxy/pulse">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
581 Pulse
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
582 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
583
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
584 </nav>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
585 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
586
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
587
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
588 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
589 <div class="container-lg new-discussion-timeline experiment-repo-nav p-responsive">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
590 <div class="repository-content ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
591
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
592
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
593
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
594
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
595
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
596
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
597
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
598 <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/johnheap/VAPPER-Galaxy/blob/a4e16d71fe985f389930c02f94354b87d3aabadb/Tryp_T.py">Permalink</a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
599
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
600 <!-- blob contrib key: blob_contributors:v21:cfb7f203d6f9590e297b1306cb3efb36 -->
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
601 <div class="signup-prompt-bg rounded-1">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
602 <div class="signup-prompt p-4 text-center mb-4 rounded-1">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
603 <div class="position-relative">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
604 <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/prompt_dismissals/signup" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="&#x2713;" /><input type="hidden" name="_method" value="put" /><input type="hidden" name="authenticity_token" value="jido5q7n2qX47et/wJYl8Tck7nSgtT9Iozz1zfwv5KasGkBWRnM0o/aO61NVISvGavRjkcTX2SsXt5o/bnBMOQ==" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
605 <button type="submit" class="position-absolute top-0 right-0 btn-link link-gray" data-ga-click="(Logged out) Sign up prompt, clicked Dismiss, text:dismiss">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
606 Dismiss
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
607 </button>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
608 </form> <h3 class="pt-2">Join GitHub today</h3>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
609 <p class="col-6 mx-auto">GitHub is home to over 36 million developers working together to host and review code, manage projects, and build software together.</p>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
610 <a class="btn btn-primary" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;files signup prompt&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;A68B:03C7:99543:10DBF9:5CF561B6&quot;,&quot;originating_url&quot;:&quot;https://github.com/johnheap/VAPPER-Galaxy/blob/master/Tryp_T.py&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="6ec2cc7ac2b87377225eea25726552c78329d919f6896791bf857db840dded2e" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up" href="/join?source=prompt-blob-show">Sign up</a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
611 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
612 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
613 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
614
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
615
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
616 <div class="d-flex flex-items-start flex-shrink-0 mb-2 flex-column flex-md-row">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
617 <span class="d-flex flex-justify-between width-full width-md-auto">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
618
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
619 <details class="details-reset details-overlay select-menu branch-select-menu hx_rsm" id="branch-select-menu">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
620 <summary class="btn btn-sm select-menu-button css-truncate"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
621 data-hotkey="w"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
622
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
623 title="Switch branches or tags">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
624 <i>Branch:</i>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
625 <span class="css-truncate-target">master</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
626 </summary>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
627
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
628 <details-menu class="select-menu-modal hx_rsm-modal position-absolute" style="z-index: 99;" src="/johnheap/VAPPER-Galaxy/ref-list/master/Tryp_T.py?source_action=show&amp;source_controller=blob" preload>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
629 <include-fragment class="select-menu-loading-overlay anim-pulse">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
630 <svg height="32" class="octicon octicon-octoface" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M14.7 5.34c.13-.32.55-1.59-.13-3.31 0 0-1.05-.33-3.44 1.3-1-.28-2.07-.32-3.13-.32s-2.13.04-3.13.32c-2.39-1.64-3.44-1.3-3.44-1.3-.68 1.72-.26 2.99-.13 3.31C.49 6.21 0 7.33 0 8.69 0 13.84 3.33 15 7.98 15S16 13.84 16 8.69c0-1.36-.49-2.48-1.3-3.35zM8 14.02c-3.3 0-5.98-.15-5.98-3.35 0-.76.38-1.48 1.02-2.07 1.07-.98 2.9-.46 4.96-.46 2.07 0 3.88-.52 4.96.46.65.59 1.02 1.3 1.02 2.07 0 3.19-2.68 3.35-5.98 3.35zM5.49 9.01c-.66 0-1.2.8-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.54-1.78-1.2-1.78zm5.02 0c-.66 0-1.2.79-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.53-1.78-1.2-1.78z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
631 </include-fragment>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
632 </details-menu>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
633 </details>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
634
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
635 <div class="BtnGroup flex-shrink-0 d-md-none">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
636 <a href="/johnheap/VAPPER-Galaxy/find/master"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
637 class="js-pjax-capture-input btn btn-sm BtnGroup-item"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
638 data-pjax
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
639 data-hotkey="t">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
640 Find file
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
641 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
642 <clipboard-copy value="Tryp_T.py" class="btn btn-sm BtnGroup-item">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
643 Copy path
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
644 </clipboard-copy>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
645 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
646 </span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
647 <h2 id="blob-path" class="breadcrumb flex-auto min-width-0 text-normal flex-md-self-center ml-md-2 mr-md-3 my-2 my-md-0">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
648 <span class="js-repo-root text-bold"><span class="js-path-segment"><a data-pjax="true" href="/johnheap/VAPPER-Galaxy"><span>VAPPER-Galaxy</span></a></span></span><span class="separator">/</span><strong class="final-path">Tryp_T.py</strong>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
649 </h2>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
650
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
651 <div class="BtnGroup flex-shrink-0 d-none d-md-inline-block">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
652 <a href="/johnheap/VAPPER-Galaxy/find/master"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
653 class="js-pjax-capture-input btn btn-sm BtnGroup-item"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
654 data-pjax
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
655 data-hotkey="t">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
656 Find file
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
657 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
658 <clipboard-copy value="Tryp_T.py" class="btn btn-sm BtnGroup-item">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
659 Copy path
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
660 </clipboard-copy>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
661 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
662 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
663
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
664
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
665
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
666 <include-fragment src="/johnheap/VAPPER-Galaxy/contributors/master/Tryp_T.py" class="Box Box--condensed commit-loader">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
667 <div class="Box-body bg-blue-light f6">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
668 Fetching contributors&hellip;
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
669 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
670
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
671 <div class="Box-body d-flex flex-items-center" >
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
672 <img alt="" class="loader-loading mr-2" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
673 <span class="text-red h6 loader-error">Cannot retrieve contributors at this time</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
674 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
675 </include-fragment>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
676
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
677
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
678
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
679
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
680
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
681 <div class="Box mt-3 position-relative">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
682
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
683 <div class="Box-header py-2 d-flex flex-column flex-shrink-0 flex-md-row flex-md-items-center">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
684
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
685 <div class="text-mono f6 flex-auto pr-3 flex-order-2 flex-md-order-1 mt-2 mt-md-0">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
686 346 lines (301 sloc)
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
687 <span class="file-info-divider"></span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
688 15 KB
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
689 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
690
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
691 <div class="d-flex py-1 py-md-0 flex-auto flex-order-1 flex-md-order-2 flex-sm-grow-0 flex-justify-between">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
692
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
693 <div class="BtnGroup">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
694 <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/raw/master/Tryp_T.py">Raw</a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
695 <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/johnheap/VAPPER-Galaxy/blame/master/Tryp_T.py">Blame</a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
696 <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/johnheap/VAPPER-Galaxy/commits/master/Tryp_T.py">History</a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
697 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
698
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
699
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
700 <div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
701
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
702 <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
703 aria-label="You must be signed in to make or propose changes">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
704 <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
705 </button>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
706 <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw"
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
707 aria-label="You must be signed in to make or propose changes">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
708 <svg class="octicon octicon-trashcan" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
709 </button>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
710 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
711 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
712 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
713
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
714
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
715
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
716 <div itemprop="text" class="Box-body p-0 blob-wrapper data type-python ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
717
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
718 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
719 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
720 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
722 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
723 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
724 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
725 <td id="LC2" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2018 University of Liverpool</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
726 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
727 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
728 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
730 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
731 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
734 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
735 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
736 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
737 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
738 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
739 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
742 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
743 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
745 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
746 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
747 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
749 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
750 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
751 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
753 <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
754 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
755 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
758 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
759 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
762 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
763 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
766 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
767 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
769 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
770 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
771 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
773 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
774 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
775 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
777 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
778 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
779 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
782 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
783 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
786 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
787 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
790 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
791 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
793 <td id="LC19" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
794 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
795 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
796 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
797 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
798 <td id="LC20" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
799 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
800 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
801 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
802 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
803 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
804 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
805 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
806 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
807 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
808 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
809 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
810 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
811 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
812 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
813 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
814 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
815 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
816 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
817 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
818 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
819 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
820 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
821 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
822 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
823 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib <span class="pl-k">as</span> mpl</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
824 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
825 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
826 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
827 <td id="LC27" 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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
828 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
829 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
830 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
831 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
832 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
833 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
834 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
835 <td id="LC29" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
836 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
837 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
838 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
839 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
840 <td id="LC30" class="blob-code blob-code-inner js-file-line">pList <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>P1<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P2<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P3<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P4<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P5<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P6<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P7<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P8<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P9<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P10<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P11<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P12<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P13<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P14<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>P15<span class="pl-pds">&#39;</span></span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
841 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
842 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
843 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
844 <td id="LC31" class="blob-code blob-code-inner js-file-line">quietString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span> <span class="pl-c"><span class="pl-c">#</span>&quot;&quot;&gt;&gt; Vap_log.txt 2&gt;&amp;1&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
845 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
846 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
847 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
848 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptMapping</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">strain</span>, <span class="pl-smi">forwardFN</span>,<span class="pl-smi">reverseFN</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
849 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
850 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
851 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
852 <td id="LC33" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>where is our Reference data -</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
853 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
854 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
855 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
856 <td id="LC34" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
857 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
858 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
859 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
860 <td id="LC35" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/Tc148<span class="pl-pds">&quot;</span></span> <span class="pl-c"><span class="pl-c">#</span>default</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
861 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
862 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
863 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
864 <td id="LC36" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
865 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
866 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
867 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
868 <td id="LC37" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/Tc148<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
869 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
870 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
871 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
872 <td id="LC38" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
873 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
874 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
875 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
876 <td id="LC39" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/IL3000<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
877 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
878 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
879 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
880 <td id="LC40" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;bowtie2 -x Refe4rence/IL3000 -1 data/&quot;+forwardFN+&quot; -2 data/&quot;+reverseFN+&quot; -S &quot;+inputname+&quot;.sam&quot; #&gt;log.txt</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
881 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
882 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
883 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
884 <td id="LC41" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;bowtie2 -x Reference/Tc148 -1 data/&quot;+forwardFN+&quot; -2 data/&quot;+reverseFN+&quot; -S &quot;+inputname+&quot;.sam&quot; #&gt;log.txt</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
885 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
886 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
887 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
888 <td id="LC42" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>bowtie2 -x <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -1 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>forwardFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -2 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>reverseFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -S <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sam<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString <span class="pl-c"><span class="pl-c">#</span>&gt;log.txt</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
889 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
890 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
891 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
892 <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(argString)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
893 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
894 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
895 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
896 <td id="LC44" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
897 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
898 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
899 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
900 <td id="LC45" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
901 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
902 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
903 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
904 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
905 <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">processSamFiles</span>(<span class="pl-smi">inputname</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
906 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
907 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
908 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
909 <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>debug use a mapping sam file we have already found</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
910 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
911 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
912 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
913 <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>dir_path = os.path.dirname(os.path.realpath(__file__))</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
914 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
915 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
916 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
917 <td id="LC49" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>bugName = dir_path+&quot;/data/T_Test&quot; #defasult</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
918 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
919 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
920 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
921 <td id="LC50" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
922 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
923 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
924 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
925 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
926 <td id="LC51" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
927 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
928 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
929 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
930 <td id="LC52" class="blob-code blob-code-inner js-file-line"> samName <span class="pl-k">=</span> cur_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>/<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
931 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
932 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
933 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
934 <td id="LC53" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
935 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
936 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
937 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
938 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
939 <td id="LC54" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;samtools view -bS &quot;+bugName+&quot; &gt; &quot;+inputname+&quot;.bam&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
940 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
941 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
942 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
943 <td id="LC55" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools view -bS <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sam &gt; <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.bam<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
944 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
945 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
946 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
947 <td id="LC56" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(argString)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
948 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
949 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
950 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
951 <td id="LC57" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
952 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
953 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
954 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
955 <td id="LC58" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
956 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
957 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
958 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
959 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
960 <td id="LC59" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
961 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
962 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
963 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
964 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
965 <td id="LC60" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;samtools sort &quot;+bugName+&quot; -o &quot;+inputname+&quot;.sorted&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
966 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
967 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
968 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
969 <td id="LC61" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools sort <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.bam -o <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
970 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
971 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
972 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
973 <td id="LC62" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;argstring = &quot;+argString)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
974 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
975 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
976 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
977 <td id="LC63" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
978 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
979 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
980 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
981 <td id="LC64" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
982 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
983 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
984 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
985 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
986 <td id="LC65" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;samtools index &quot;+bugName+&quot;.sorted &quot;+inputname+&quot;.sorted.bai&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
987 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
988 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
989 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
990 <td id="LC66" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>samtools index <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted.bai<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
991 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
992 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
993 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
994 <td id="LC67" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;argstring = &quot; + argString)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
995 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
996 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
997 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
998 <td id="LC68" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
999 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1000 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1001 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1002 <td id="LC69" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1003 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1004 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1005 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1006 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1007 <td id="LC70" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1008 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1009 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1010 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1011 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1012 <td id="LC71" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1013 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1014 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1015 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1016 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1017 <td id="LC72" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1018 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1019 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1020 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1021 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1022 <td id="LC73" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptAbundance</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">strain</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1023 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1024 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1025 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1026 <td id="LC74" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1027 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1028 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1029 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1030 <td id="LC75" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">&quot;</span></span> <span class="pl-c"><span class="pl-c">#</span> defasult</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1031 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1032 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1033 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1034 <td id="LC76" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1035 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1036 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1037 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1038 <td id="LC77" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1039 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1040 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1041 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1042 <td id="LC78" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1043 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1044 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1045 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1046 <td id="LC79" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/IL3000.gtf<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1047 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1048 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1049 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1050 <td id="LC80" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;cufflinks -G Reference/IL3000.gtf -o &quot;+inputname+&quot;.cuff -u -p 8 &quot;+inputname+&quot;.sorted&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1051 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1052 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1053 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1054 <td id="LC81" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>argString = &quot;cufflinks -G Reference/ORFAnnotation.gtf -o &quot;+inputname+&quot;.cuff -u -p 8 &quot;+inputname+&quot;.sorted&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1055 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1056 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1057 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1058 <td id="LC82" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>cufflinks -q -G <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> -o <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.cuff -u -p 8 <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.sorted<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>quietString</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1059 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1060 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1061 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1062 <td id="LC83" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1063 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1064 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1065 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1066 <td id="LC84" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1067 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1068 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1069 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1070 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1071 <td id="LC85" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1072 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1073 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1074 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1075 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1076 <td id="LC86" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">convertToFasta</span>(<span class="pl-smi">inputName</span>, <span class="pl-smi">strain</span>): <span class="pl-c"><span class="pl-c">#</span>equivalent to Sara&#39;s awk scripte</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1077 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1078 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1079 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1080 <td id="LC87" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1081 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1082 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1083 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1084 <td id="LC88" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/ORFAnnotation.gtf<span class="pl-pds">&quot;</span></span> <span class="pl-c"><span class="pl-c">#</span> default</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1085 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1086 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1087 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1088 <td id="LC89" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1089 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1090 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1091 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1092 <td id="LC90" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/148_prot.fasta<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1093 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1094 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1095 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1096 <td id="LC91" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1097 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1098 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1099 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1100 <td id="LC92" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Reference/IL3000_prot.fasta<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1101 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1102 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1103 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1104 <td id="LC93" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1105 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1106 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1107 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1108 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1109 <td id="LC94" class="blob-code blob-code-inner js-file-line"> cuff_df <span class="pl-k">=</span> pd.read_csv(inputName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>.cuff/genes.fpkm_tracking<span class="pl-pds">&quot;</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span><span class="pl-cce">\t</span><span class="pl-pds">&#39;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1110 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1111 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1112 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1113 <td id="LC95" class="blob-code blob-code-inner js-file-line"> cuff_df <span class="pl-k">=</span> cuff_df[(cuff_df[<span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>] <span class="pl-k">&gt;</span> <span class="pl-c1">0</span>)]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1114 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1115 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1116 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1117 <td id="LC96" class="blob-code blob-code-inner js-file-line"> cuff_df.to_csv(<span class="pl-s"><span class="pl-pds">&quot;</span>cuffTest.csv<span class="pl-pds">&quot;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1118 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1119 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1120 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1121 <td id="LC97" class="blob-code blob-code-inner js-file-line"> gene_id_List <span class="pl-k">=</span> cuff_df[<span class="pl-s"><span class="pl-pds">&#39;</span>gene_id<span class="pl-pds">&#39;</span></span>].tolist()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1122 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1123 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1124 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1125 <td id="LC98" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1126 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1127 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1128 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1129 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1130 <td id="LC99" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(gene_id_List)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1131 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1132 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1133 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1134 <td id="LC100" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (&quot;Found from 8880=&quot;+str(found))</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1135 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1136 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1137 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1138 <td id="LC101" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1139 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1140 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1141 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1142 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1143 <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> need to load in IL3000_prot.fasta</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1144 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1145 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1146 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1147 <td id="LC103" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> for each line with &gt;TcIL3000_1_1940</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1148 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1149 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1150 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1151 <td id="LC104" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> search within cuff_df[gene_id] for match</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1152 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1153 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1154 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1155 <td id="LC105" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> add it to the outfile. (need to save it as used by hmmer later</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1156 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1157 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1158 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1159 <td id="LC106" class="blob-code blob-code-inner js-file-line"> number <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1160 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1161 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1162 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1163 <td id="LC107" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">all</span> <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1164 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1165 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1166 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1167 <td id="LC108" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(inputName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>_6frame.fas<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>w<span class="pl-pds">&#39;</span></span>) <span class="pl-k">as</span> outfile:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1168 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1169 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1170 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1171 <td id="LC109" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> <span class="pl-c1">open</span>(refName,<span class="pl-s"><span class="pl-pds">&#39;</span>r<span class="pl-pds">&#39;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1172 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1173 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1174 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1175 <td id="LC110" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>ref = open(r&quot;Reference/IL3000_prot.fasta&quot;,&#39;r&#39;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1176 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1177 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1178 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1179 <td id="LC111" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1180 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1181 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1182 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1183 <td id="LC112" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1184 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1185 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1186 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1187 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">while</span> line:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1188 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1189 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1190 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1191 <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line[<span class="pl-c1">0</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>&gt;<span class="pl-pds">&#39;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1192 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1193 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1194 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1195 <td id="LC115" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">all</span> <span class="pl-k">=</span> <span class="pl-c1">all</span><span class="pl-k">+</span><span class="pl-c1">1</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1196 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1197 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1198 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1199 <td id="LC116" class="blob-code blob-code-inner js-file-line"> ln <span class="pl-k">=</span> line[<span class="pl-c1">1</span>:] <span class="pl-c"><span class="pl-c">#</span>remove &gt;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1200 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1201 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1202 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1203 <td id="LC117" class="blob-code blob-code-inner js-file-line"> ln <span class="pl-k">=</span> ln.rstrip() <span class="pl-c"><span class="pl-c">#</span>remove /n /r etc</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1204 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1205 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1206 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1207 <td id="LC118" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (ln)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1208 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1209 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1210 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1211 <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> ln <span class="pl-k">in</span> gene_id_List:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1212 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1213 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1214 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1215 <td id="LC120" class="blob-code blob-code-inner js-file-line"> number <span class="pl-k">=</span> number<span class="pl-k">+</span><span class="pl-c1">1</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1216 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1217 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1218 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1219 <td id="LC121" class="blob-code blob-code-inner js-file-line"> outfile.write(line)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1220 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1221 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1222 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1223 <td id="LC122" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1224 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1225 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1226 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1227 <td id="LC123" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> line:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1228 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1229 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1230 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1231 <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">while</span> line[<span class="pl-c1">0</span>] <span class="pl-k">!=</span> <span class="pl-s"><span class="pl-pds">&#39;</span>&gt;<span class="pl-pds">&#39;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1232 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1233 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1234 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1235 <td id="LC125" class="blob-code blob-code-inner js-file-line"> outfile.write(line)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1236 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1237 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1238 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1239 <td id="LC126" class="blob-code blob-code-inner js-file-line"> line<span class="pl-k">=</span>ref.readline()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1240 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1241 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1242 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1243 <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-k">not</span> line:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1244 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1245 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1246 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1247 <td id="LC128" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span><span class="pl-bu">;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1248 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1249 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1250 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1251 <td id="LC129" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1252 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1253 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1254 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1255 <td id="LC130" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span> ref.readline()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1256 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1257 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1258 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1259 <td id="LC131" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1260 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1261 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1262 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1263 <td id="LC132" class="blob-code blob-code-inner js-file-line"> line <span class="pl-k">=</span>ref.readline()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1264 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1265 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1266 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1267 <td id="LC133" class="blob-code blob-code-inner js-file-line"> ref.close()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1268 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1269 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1270 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1271 <td id="LC134" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-c1">str</span>(<span class="pl-c1">len</span>(gene_id_List))<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span>:<span class="pl-pds">&quot;</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(number)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">&quot;</span> from <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(<span class="pl-c1">all</span>))</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1272 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1273 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1274 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1275 <td id="LC135" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> cuff_df</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1276 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1277 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1278 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1279 <td id="LC136" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1280 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1281 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1282 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1283 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1284 <td id="LC137" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">HMMerMotifSearch</span>(<span class="pl-smi">name</span>, <span class="pl-smi">strain</span>, <span class="pl-smi">cuff_df</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1285 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1286 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1287 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1288 <td id="LC138" class="blob-code blob-code-inner js-file-line"> motifs <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&#39;</span>1<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>2a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>2b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>3<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>4c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>5<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>6<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>7<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>8a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>8b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>9a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>9b<span class="pl-pds">&#39;</span></span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1289 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1290 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1291 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1292 <td id="LC139" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&#39;</span>9c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>10a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>10b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>11a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>11b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>12<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13c<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>13d<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>14<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15a<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15b<span class="pl-pds">&#39;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>15c<span class="pl-pds">&#39;</span></span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1293 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1294 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1295 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1296 <td id="LC140" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1297 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1298 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1299 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1300 <td id="LC141" class="blob-code blob-code-inner js-file-line"> phylopath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/data/Motifs/Phylotype<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1301 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1302 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1303 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1304 <td id="LC142" class="blob-code blob-code-inner js-file-line"> lineCounts <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1305 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1306 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1307 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1308 <td id="LC143" class="blob-code blob-code-inner js-file-line"> compoundList <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1309 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1310 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1311 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1312 <td id="LC144" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> m <span class="pl-k">in</span> motifs:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1313 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1314 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1315 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1316 <td id="LC145" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>hmmsearch <span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>phylopath <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.hmm <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>_6frame.fas &gt; Phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.out<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1317 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1318 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1319 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1320 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1321 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1322 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1323 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1324 <td id="LC147" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1325 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1326 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1327 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1328 <td id="LC148" class="blob-code blob-code-inner js-file-line"> hmmResult <span class="pl-k">=</span> <span class="pl-c1">open</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>Phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> m <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>.out<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&#39;</span>r<span class="pl-pds">&#39;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1329 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1330 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1331 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1332 <td id="LC149" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>Tc148[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,8}</span><span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1333 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1334 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1335 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1336 <td id="LC150" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1337 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1338 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1339 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1340 <td id="LC151" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>Tc148[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,8}</span><span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1341 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1342 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1343 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1344 <td id="LC152" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1345 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1346 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1347 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1348 <td id="LC153" class="blob-code blob-code-inner js-file-line"> regex <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>TcIL3000_[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,4}</span>_[<span class="pl-c1">0-9</span>]<span class="pl-k">{1,5}</span><span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1349 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1350 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1351 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1352 <td id="LC154" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1353 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1354 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1355 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1356 <td id="LC155" class="blob-code blob-code-inner js-file-line"> outList <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1357 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1358 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1359 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1360 <td id="LC156" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> line <span class="pl-k">in</span> hmmResult:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1361 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1362 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1363 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1364 <td id="LC157" class="blob-code blob-code-inner js-file-line"> m <span class="pl-k">=</span> re.search(regex, line)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1365 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1366 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1367 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1368 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> m:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1369 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1370 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1371 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1372 <td id="LC159" class="blob-code blob-code-inner js-file-line"> outList.append(<span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span><span class="pl-k">+</span>m.group())</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1373 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1374 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1375 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1376 <td id="LC160" class="blob-code blob-code-inner js-file-line"> n <span class="pl-k">+=</span> <span class="pl-c1">1</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1377 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1378 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1379 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1380 <td id="LC161" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> re.search(<span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>inclusion<span class="pl-pds">&quot;</span></span>, line):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1381 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1382 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1383 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1384 <td id="LC162" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>inclusion threshold reached<span class="pl-pds">&quot;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1385 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1386 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1387 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1388 <td id="LC163" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">break</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1389 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1390 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1391 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1392 <td id="LC164" class="blob-code blob-code-inner js-file-line"> compoundList.append(outList)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1393 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1394 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1395 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1396 <td id="LC165" class="blob-code blob-code-inner js-file-line"> lineCounts.append(n)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1397 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1398 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1399 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1400 <td id="LC166" class="blob-code blob-code-inner js-file-line"> hmmResult.close()</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1401 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1402 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1403 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1404 <td id="LC167" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(lineCounts)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1405 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1406 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1407 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1408 <td id="LC168" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1409 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1410 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1411 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1412 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1413 <td id="LC169" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(cuff_df)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1414 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1415 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1416 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1417 <td id="LC170" class="blob-code blob-code-inner js-file-line"> concatGroups <span class="pl-k">=</span> [<span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">1</span>, <span class="pl-c1">2</span>, <span class="pl-c1">3</span>, <span class="pl-c1">2</span>, <span class="pl-c1">2</span>, <span class="pl-c1">1</span>, <span class="pl-c1">4</span>, <span class="pl-c1">1</span>, <span class="pl-c1">3</span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1418 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1419 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1420 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1421 <td id="LC171" class="blob-code blob-code-inner js-file-line"> countList <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1422 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1423 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1424 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1425 <td id="LC172" class="blob-code blob-code-inner js-file-line"> weightList <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1426 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1427 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1428 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1429 <td id="LC173" class="blob-code blob-code-inner js-file-line"> countIndex <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1430 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1431 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1432 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1433 <td id="LC174" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1434 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1435 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1436 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1437 <td id="LC175" class="blob-code blob-code-inner js-file-line"> totalWeigth <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1438 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1439 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1440 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1441 <td id="LC176" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> c <span class="pl-k">in</span> concatGroups:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1442 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1443 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1444 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1445 <td id="LC177" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1446 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1447 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1448 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1449 <td id="LC178" class="blob-code blob-code-inner js-file-line"> weight <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1450 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1451 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1452 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1453 <td id="LC179" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, c):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1454 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1455 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1456 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1457 <td id="LC180" class="blob-code blob-code-inner js-file-line"> a <span class="pl-k">=</span> a <span class="pl-k">+</span> compoundList.pop(<span class="pl-c1">0</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1458 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1459 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1460 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1461 <td id="LC181" class="blob-code blob-code-inner js-file-line"> t <span class="pl-k">=</span> <span class="pl-c1">set</span>(a)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1462 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1463 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1464 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1465 <td id="LC182" class="blob-code blob-code-inner js-file-line"> countList.append(<span class="pl-c1">len</span>(t))</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1466 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1467 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1468 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1469 <td id="LC183" class="blob-code blob-code-inner js-file-line"> wa <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1470 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1471 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1472 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1473 <td id="LC184" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> w <span class="pl-k">in</span> t:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1474 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1475 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1476 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1477 <td id="LC185" class="blob-code blob-code-inner js-file-line"> wt <span class="pl-k">=</span> cuff_df.loc[cuff_df[<span class="pl-s"><span class="pl-pds">&#39;</span>gene_id<span class="pl-pds">&#39;</span></span>] <span class="pl-k">==</span> w, <span class="pl-s"><span class="pl-pds">&#39;</span>FPKM<span class="pl-pds">&#39;</span></span>].iloc[<span class="pl-c1">0</span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1478 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1479 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1480 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1481 <td id="LC186" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(w)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1482 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1483 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1484 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1485 <td id="LC187" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(wt)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1486 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1487 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1488 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1489 <td id="LC188" class="blob-code blob-code-inner js-file-line"> wa <span class="pl-k">=</span> wa<span class="pl-k">+</span>wt</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1490 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1491 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1492 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1493 <td id="LC189" class="blob-code blob-code-inner js-file-line"> weightList.append(wa)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1494 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1495 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1496 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1497 <td id="LC190" class="blob-code blob-code-inner js-file-line"> totalWeigth<span class="pl-k">+=</span>wa</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1498 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1499 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1500 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1501 <td id="LC191" class="blob-code blob-code-inner js-file-line"> totalCount <span class="pl-k">+=</span> <span class="pl-c1">len</span>(t)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1502 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1503 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1504 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1505 <td id="LC192" class="blob-code blob-code-inner js-file-line"> countList.append(totalCount)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1506 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1507 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1508 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1509 <td id="LC193" class="blob-code blob-code-inner js-file-line"> weightList.append(totalWeigth)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1510 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1511 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1512 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1513 <td id="LC194" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(countList)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1514 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1515 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1516 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1517 <td id="LC195" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;--------&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1518 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1519 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1520 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1521 <td id="LC196" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(weightList)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1522 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1523 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1524 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1525 <td id="LC197" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;--------&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1526 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1527 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1528 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1529 <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> countList,weightList</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1530 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1531 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1532 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1533 <td id="LC199" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1534 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1535 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1536 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1537 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1538 <td id="LC200" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">relativeFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1539 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1540 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1541 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1542 <td id="LC201" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1543 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1544 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1545 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1546 <td id="LC202" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</span>])</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1547 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1548 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1549 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1550 <td id="LC203" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1551 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1552 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1553 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1554 <td id="LC204" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1555 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1556 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1557 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1558 <td id="LC205" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1559 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1560 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1561 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1562 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1563 <td id="LC206" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>: pList, <span class="pl-s"><span class="pl-pds">&#39;</span>Relative Frequency<span class="pl-pds">&#39;</span></span>: relFreqList}</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1564 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1565 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1566 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1567 <td id="LC207" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1568 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1569 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1570 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1571 <td id="LC208" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> htmlresource<span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&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>_t_relative_frequency.csv<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1572 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1573 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1574 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1575 <td id="LC209" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1576 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1577 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1578 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1579 <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> relFreqList <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1580 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1581 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1582 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1583 <td id="LC211" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1584 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1585 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1586 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1587 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1588 <td id="LC212" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1589 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1590 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1591 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1592 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1593 <td id="LC213" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">weightedFrequencyTable</span>(<span class="pl-smi">countList</span>, <span class="pl-smi">name</span>, <span class="pl-smi">htmlresource</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1594 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1595 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1596 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1597 <td id="LC214" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1598 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1599 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1600 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1601 <td id="LC215" class="blob-code blob-code-inner js-file-line"> c <span class="pl-k">=</span> <span class="pl-c1">float</span>(countList[<span class="pl-c1">15</span>])</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1602 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1603 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1604 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1605 <td id="LC216" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1606 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1607 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1608 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1609 <td id="LC217" class="blob-code blob-code-inner js-file-line"> relFreqList.append(countList[i] <span class="pl-k">/</span> c)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1610 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1611 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1612 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1613 <td id="LC218" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1614 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1615 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1616 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1617 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1618 <td id="LC219" class="blob-code blob-code-inner js-file-line"> data <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>Phylotype<span class="pl-pds">&#39;</span></span>: pList, <span class="pl-s"><span class="pl-pds">&#39;</span>Weighted Frequency<span class="pl-pds">&#39;</span></span>: relFreqList}</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1619 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1620 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1621 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1622 <td id="LC220" class="blob-code blob-code-inner js-file-line"> relFreq_df <span class="pl-k">=</span> pd.DataFrame(data)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1623 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1624 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1625 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1626 <td id="LC221" class="blob-code blob-code-inner js-file-line"> j_fname <span class="pl-k">=</span> htmlresource<span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&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>_t_weighted_frequency.csv<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1627 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1628 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1629 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1630 <td id="LC222" class="blob-code blob-code-inner js-file-line"> relFreq_df.to_csv(j_fname)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1631 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1632 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1633 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1634 <td id="LC223" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> relFreqList <span class="pl-c"><span class="pl-c">#</span> 0-14 = p1-p15 counts [15] = total counts</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1635 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1636 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1637 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1638 <td id="LC224" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1639 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1640 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1641 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1642 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1643 <td id="LC225" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1644 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1645 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1646 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1647 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1648 <td id="LC226" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1649 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1650 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1651 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1652 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1653 <td id="LC227" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createStackedBar</span>(<span class="pl-smi">name</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">strain</span>,<span class="pl-smi">pdf</span>,<span class="pl-smi">html_resource</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1654 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1655 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1656 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1657 <td id="LC228" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">&quot;</span>#0000ff<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#6495ed<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#00ffff<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#caff70<span class="pl-pds">&quot;</span></span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1658 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1659 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1660 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1661 <td id="LC229" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>#228b22<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#528b8b<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#00ff00<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#a52a2a<span class="pl-pds">&quot;</span></span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1662 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1663 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1664 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1665 <td id="LC230" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>#ff0000<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#ffff00<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#ffa500<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#ff1493<span class="pl-pds">&quot;</span></span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1666 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1667 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1668 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1669 <td id="LC231" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>#9400d3<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#bebebe<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#000000<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>#ff00ff<span class="pl-pds">&quot;</span></span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1670 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1671 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1672 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1673 <td id="LC232" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1674 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1675 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1676 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1677 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1678 <td id="LC233" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">VAP_148</span> <span class="pl-k">=</span> [<span class="pl-c1">0.072</span>, <span class="pl-c1">0.032</span>, <span class="pl-c1">0.032</span>, <span class="pl-c1">0.004</span>, <span class="pl-c1">0.007</span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1679 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1680 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1681 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1682 <td id="LC234" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.005</span>, <span class="pl-c1">0.202</span>, <span class="pl-c1">0.004</span>, <span class="pl-c1">0.006</span>, <span class="pl-c1">0.014</span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1683 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1684 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1685 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1686 <td id="LC235" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.130</span>, <span class="pl-c1">0.133</span>, <span class="pl-c1">0.054</span>, <span class="pl-c1">0.039</span>, <span class="pl-c1">0.265</span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1687 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1688 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1689 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1690 <td id="LC236" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1691 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1692 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1693 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1694 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1695 <td id="LC237" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">VAP_IL3000</span> <span class="pl-k">=</span> [<span class="pl-c1">0.073</span>, <span class="pl-c1">0.040</span>, <span class="pl-c1">0.049</span>, <span class="pl-c1">0.018</span>, <span class="pl-c1">0.060</span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1696 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1697 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1698 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1699 <td id="LC238" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.055</span>, <span class="pl-c1">0.054</span>, <span class="pl-c1">0.025</span>, <span class="pl-c1">0.012</span>, <span class="pl-c1">0.060</span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1700 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1701 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1702 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1703 <td id="LC239" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.142</span>, <span class="pl-c1">0.100</span>, <span class="pl-c1">0.061</span>, <span class="pl-c1">0.078</span>, <span class="pl-c1">0.172</span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1704 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1705 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1706 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1707 <td id="LC240" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">&#39;</span>tab20<span class="pl-pds">&#39;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1708 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1709 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1710 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1711 <td id="LC241" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1712 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1713 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1714 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1715 <td id="LC242" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1716 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1717 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1718 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1719 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1720 <td id="LC243" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Tc148<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1721 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1722 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1723 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1724 <td id="LC244" class="blob-code blob-code-inner js-file-line"> VAPtable <span class="pl-k">=</span> <span class="pl-c1">VAP_148</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1725 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1726 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1727 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1728 <td id="LC245" class="blob-code blob-code-inner js-file-line"> VAPname<span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&#39;</span>Tc148<span class="pl-cce">\n</span>Genome VAP<span class="pl-pds">&#39;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1729 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1730 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1731 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1732 <td id="LC246" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> strain <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>IL3000<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1733 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1734 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1735 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1736 <td id="LC247" class="blob-code blob-code-inner js-file-line"> VAPtable <span class="pl-k">=</span> <span class="pl-c1">VAP_IL3000</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1737 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1738 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1739 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1740 <td id="LC248" class="blob-code blob-code-inner js-file-line"> VAPname<span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&#39;</span>IL3000<span class="pl-cce">\n</span>Genome VAP<span class="pl-pds">&#39;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1741 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1742 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1743 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1744 <td id="LC249" class="blob-code blob-code-inner js-file-line"> width <span class="pl-k">=</span> <span class="pl-c1">0.35</span> <span class="pl-c"><span class="pl-c">#</span> the width of the bars: can also be len(x) sequence</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1745 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1746 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1747 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1748 <td id="LC250" class="blob-code blob-code-inner js-file-line"> plots <span class="pl-k">=</span> []</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1749 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1750 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1751 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1752 <td id="LC251" class="blob-code blob-code-inner js-file-line"> fpos <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1753 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1754 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1755 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1756 <td id="LC252" class="blob-code blob-code-inner js-file-line"> vpos <span class="pl-k">=</span> <span class="pl-c1">0</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1757 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1758 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1759 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1760 <td id="LC253" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1761 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1762 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1763 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1764 <td id="LC254" class="blob-code blob-code-inner js-file-line"> tp <span class="pl-k">=</span> plt.bar(<span class="pl-c1">0</span>, freqList[p], width, <span class="pl-v">color</span><span class="pl-k">=</span> palette[p], <span class="pl-v">bottom</span> <span class="pl-k">=</span> fpos)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1765 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1766 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1767 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1768 <td id="LC255" class="blob-code blob-code-inner js-file-line"> fpos <span class="pl-k">+=</span>freqList[p]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1769 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1770 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1771 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1772 <td id="LC256" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1773 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1774 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1775 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1776 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1777 <td id="LC257" class="blob-code blob-code-inner js-file-line"> tp <span class="pl-k">=</span> plt.bar(<span class="pl-c1">1</span>, VAPtable[p], width, <span class="pl-v">color</span><span class="pl-k">=</span> palette[p], <span class="pl-v">bottom</span> <span class="pl-k">=</span> vpos)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1778 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1779 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1780 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1781 <td id="LC258" class="blob-code blob-code-inner js-file-line"> vpos <span class="pl-k">+=</span>VAPtable[p]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1782 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1783 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1784 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1785 <td id="LC259" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1786 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1787 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1788 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1789 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1790 <td id="LC260" class="blob-code blob-code-inner js-file-line"> plots.append(tp)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1791 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1792 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1793 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1794 <td id="LC261" class="blob-code blob-code-inner js-file-line"> plt.xticks([<span class="pl-c1">0</span>,<span class="pl-c1">1</span>],[name,VAPname])</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1795 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1796 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1797 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1798 <td id="LC262" class="blob-code blob-code-inner js-file-line"> plt.legend(plots[::<span class="pl-k">-</span><span class="pl-c1">1</span>],[<span class="pl-s"><span class="pl-pds">&#39;</span>p15<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p14<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p13<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p12<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p11<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p10<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p9<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p8<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p7<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p6<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p5<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p4<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p3<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p2<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>p1<span class="pl-pds">&#39;</span></span>])</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1799 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1800 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1801 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1802 <td id="LC263" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Figure Legend: The transcriptomic Variant Antigen Profile of $\itTrypanosoma$ $\itcongolense$ estimated as phylotype <span class="pl-pds">&quot;</span></span> \</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1803 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1804 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1805 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1806 <td id="LC264" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>proportion adjusted for transcript abundance and the reference genomic Variant Antigen Profile. <span class="pl-pds">&quot;</span></span> \</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1807 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1808 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1809 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1810 <td id="LC265" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span>Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1811 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1812 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1813 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1814 <td id="LC266" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.title(title, wrap=&quot;True&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1815 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1816 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1817 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1818 <td id="LC267" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.text(-0.2, -0.05, title, va=&quot;top&quot;, transform=ax.transAxes, wrap=&quot;True&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1819 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1820 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1821 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1822 <td id="LC268" class="blob-code blob-code-inner js-file-line"> plt.text(<span class="pl-k">-</span><span class="pl-c1">0.3</span>, <span class="pl-k">-</span><span class="pl-c1">0.15</span>, title, <span class="pl-v">va</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&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>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1823 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1824 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1825 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1826 <td id="LC269" class="blob-code blob-code-inner js-file-line"> plt.tight_layout(<span class="pl-v">pad</span><span class="pl-k">=</span><span class="pl-c1">1.5</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1827 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1828 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1829 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1830 <td id="LC270" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span> <span class="pl-k">=</span> <span class="pl-c1">0.3</span>,<span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.99</span>,<span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.125</span>,<span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>,<span class="pl-v">hspace</span><span class="pl-k">=</span><span class="pl-c1">0.2</span>,<span class="pl-v">wspace</span><span class="pl-k">=</span><span class="pl-c1">0.2</span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1831 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1832 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1833 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1834 <td id="LC271" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1835 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1836 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1837 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1838 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1839 <td id="LC272" class="blob-code blob-code-inner js-file-line"> plt.savefig(html_resource <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/stackedbar.png<span class="pl-pds">&quot;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1840 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1841 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1842 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1843 <td id="LC273" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> pdf <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1844 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1845 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1846 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1847 <td id="LC274" class="blob-code blob-code-inner js-file-line"> plt.savefig(html_resource <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>/stackedbar.pdf<span class="pl-pds">&quot;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1848 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1849 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1850 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1851 <td id="LC275" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.show()</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1852 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1853 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1854 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1855 <td id="LC276" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1856 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1857 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1858 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1859 <td id="L277" class="blob-num js-line-number" data-line-number="277"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1860 <td id="LC277" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1861 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1862 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1863 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1864 <td id="L278" class="blob-num js-line-number" data-line-number="278"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1865 <td id="LC278" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">name</span>,<span class="pl-smi">htmlfn</span>,<span class="pl-smi">htmlresource</span>,<span class="pl-smi">freqList</span>,<span class="pl-smi">weightList</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1866 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1867 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1868 <td id="L279" class="blob-num js-line-number" data-line-number="279"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1869 <td id="LC279" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1870 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1871 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1872 <td id="L280" class="blob-num js-line-number" data-line-number="280"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1873 <td id="LC280" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;html&gt;&lt;title&gt;T<span class="pl-c1">.</span>congolense VAP&lt;/title&gt;&lt;body&gt;&lt;div style=&#39;text-align:center&#39;&gt;&lt;h2&gt;&lt;i&gt;Trypanosoma congolense&lt;/i&gt; Variant Antigen Profile&lt;/h2&gt;&lt;h3&gt;<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1874 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1875 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1876 <td id="L281" class="blob-num js-line-number" data-line-number="281"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1877 <td id="LC281" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> name</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1878 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1879 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1880 <td id="L282" class="blob-num js-line-number" data-line-number="282"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1881 <td id="LC282" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;br&gt;Transcriptomic Analysis&lt;/h3&gt;&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1882 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1883 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1884 <td id="L283" class="blob-num js-line-number" data-line-number="283"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1885 <td id="LC283" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;p style = &#39;margin-left:20%; margin-right:20%&#39;&gt;Table Legend: Variant Antigen Profiles of a transcriptome of &lt;i&gt;Trypanosoma congolense&lt;/i&gt; estimated as phylotype proportion. <span class="pl-pds">&quot;</span></span> \</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1886 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1887 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1888 <td id="L284" class="blob-num js-line-number" data-line-number="284"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1889 <td id="LC284" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Weighted frequency refers to the phylotype proportion based transcript abundance. <span class="pl-pds">&quot;</span></span> \</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1890 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1891 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1892 <td id="L285" class="blob-num js-line-number" data-line-number="285"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1893 <td id="LC285" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">&quot;</span>Data was produced with the &#39;Variant Antigen Profiler&#39; (Silva Pereira et al., 2019).&lt;/p&gt; <span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1894 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1895 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1896 <td id="L286" class="blob-num js-line-number" data-line-number="286"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1897 <td id="LC286" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;style&gt; table, th, tr, td {border: 1px solid black; border-collapse: collapse;}&lt;/style&gt;<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1898 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1899 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1900 <td id="L287" class="blob-num js-line-number" data-line-number="287"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1901 <td id="LC287" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1902 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1903 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1904 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1905 <td id="L288" class="blob-num js-line-number" data-line-number="288"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1906 <td id="LC288" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;table style=&#39;width:50%;margin-left:25%;text-align:center&#39;&gt;&lt;tr&gt;&lt;th&gt;Phylotype&lt;/th&gt;&lt;th&gt;Relative Frequency&lt;/th&gt;&lt;th&gt;Weighted Frequency&lt;/th&gt;&lt;/tr&gt;<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1907 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1908 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1909 <td id="L289" class="blob-num js-line-number" data-line-number="289"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1910 <td id="LC289" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1911 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1912 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1913 <td id="L290" class="blob-num js-line-number" data-line-number="290"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1914 <td id="LC290" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1915 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1916 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1917 <td id="L291" class="blob-num js-line-number" data-line-number="291"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1918 <td id="LC291" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">15</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1919 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1920 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1921 <td id="L292" class="blob-num js-line-number" data-line-number="292"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1922 <td id="LC292" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(freqList[i], <span class="pl-s"><span class="pl-pds">&#39;</span>.4f<span class="pl-pds">&#39;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1923 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1924 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1925 <td id="L293" class="blob-num js-line-number" data-line-number="293"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1926 <td id="LC293" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">format</span>(weightList[i], <span class="pl-s"><span class="pl-pds">&#39;</span>.4f<span class="pl-pds">&#39;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1927 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1928 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1929 <td id="L294" class="blob-num js-line-number" data-line-number="294"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1930 <td id="LC294" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;tr&gt;&lt;td&gt;phy<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(i <span class="pl-k">+</span> <span class="pl-c1">1</span>) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> f <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;td&gt;<span class="pl-pds">&quot;</span></span> <span class="pl-k">+</span> w <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/td&gt;&lt;/tr&gt;<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1931 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1932 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1933 <td id="L295" class="blob-num js-line-number" data-line-number="295"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1934 <td id="LC295" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">&quot;</span>&lt;/table&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1935 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1936 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1937 <td id="L296" class="blob-num js-line-number" data-line-number="296"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1938 <td id="LC296" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;p&gt; &lt;h3&gt;Stacked Bar chart of Phylotype Frequency&lt;/h3&gt; The &#39;weighted&#39; relative frequency of each phylotype alongside the VAP of selected strain<span class="pl-c1">.</span>&lt;/p&gt;<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1939 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1940 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1941 <td id="L297" class="blob-num js-line-number" data-line-number="297"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1942 <td id="LC297" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">&quot;</span>&lt;img src = &#39;stackedbar<span class="pl-c1">.</span>png&#39; alt=&#39;Stacked bar chart of phylotype variation&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;<span class="pl-pds">&quot;</span></span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1943 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1944 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1945 <td id="L298" class="blob-num js-line-number" data-line-number="298"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1946 <td id="LC298" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1947 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1948 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1949 <td id="L299" class="blob-num js-line-number" data-line-number="299"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1950 <td id="LC299" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1951 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1952 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1953 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1954 <td id="L300" class="blob-num js-line-number" data-line-number="300"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1955 <td id="LC300" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += r&quot;&lt;p&gt;&lt;h3&gt;The Deviation Heat Map and Dendogram&lt;/h3&gt;The phylotype variation expressed as the deviation from your sample mean compared to the model dataset&lt;/p&gt;&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1956 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1957 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1958 <td id="L301" class="blob-num js-line-number" data-line-number="301"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1959 <td id="LC301" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> imgString = r&quot;&lt;img src = &#39;dheatmap.png&#39; alt=&#39;Deviation Heatmap&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1960 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1961 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1962 <td id="L302" class="blob-num js-line-number" data-line-number="302"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1963 <td id="LC302" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += imgString</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1964 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1965 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1966 <td id="L303" class="blob-num js-line-number" data-line-number="303"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1967 <td id="LC303" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1968 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1969 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1970 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1971 <td id="L304" class="blob-num js-line-number" data-line-number="304"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1972 <td id="LC304" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += r&quot;&lt;p&gt;&lt;h3&gt;The Variation PCA plot&lt;/h3&gt;PCA analysis corresponding to absolute variation. Colour coded according to location&lt;/p&gt;&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1973 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1974 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1975 <td id="L305" class="blob-num js-line-number" data-line-number="305"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1976 <td id="LC305" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> imgString = r&quot;&lt;img src = &#39;vapPCA.png&#39; alt=&#39;PCA Analysis&#39; style=&#39;max-width:100%&#39;&gt;&lt;br&gt;&lt;br&gt;&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1977 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1978 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1979 <td id="L306" class="blob-num js-line-number" data-line-number="306"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1980 <td id="LC306" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> htmlString += imgString + r&quot;&lt;/div&gt;&lt;/body&gt;&lt;/html&gt;&quot;</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1981 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1982 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1983 <td id="L307" class="blob-num js-line-number" data-line-number="307"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1984 <td id="LC307" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1985 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1986 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1987 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1988 <td id="L308" class="blob-num js-line-number" data-line-number="308"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1989 <td id="LC308" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(htmlfn, <span class="pl-s"><span class="pl-pds">&quot;</span>w<span class="pl-pds">&quot;</span></span>) <span class="pl-k">as</span> htmlfile:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1990 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1991 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1992 <td id="L309" class="blob-num js-line-number" data-line-number="309"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1993 <td id="LC309" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1994 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1995 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1996 <td id="L310" class="blob-num js-line-number" data-line-number="310"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1997 <td id="LC310" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1998 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
1999 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2000 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2001 <td id="L311" class="blob-num js-line-number" data-line-number="311"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2002 <td id="LC311" 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;strain&#39;: 4, &#39;forward&#39;: 5, &#39;reverse&#39;: 6, &#39;html_file&#39;: 7, &#39;html_resource&#39;: 8}</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2003 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2004 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2005 <td id="L312" class="blob-num js-line-number" data-line-number="312"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2006 <td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptomicProcess</span>(<span class="pl-smi">args</span>,<span class="pl-smi">dict</span>):</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2007 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2008 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2009 <td id="L313" class="blob-num js-line-number" data-line-number="313"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2010 <td id="LC313" class="blob-code blob-code-inner js-file-line"> transcriptMapping(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>strain<span class="pl-pds">&#39;</span></span>]], 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>]]) <span class="pl-c"><span class="pl-c">#</span>uses bowtie</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2011 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2012 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2013 <td id="L314" class="blob-num js-line-number" data-line-number="314"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2014 <td id="LC314" class="blob-code blob-code-inner js-file-line"> processSamFiles(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>uses samtools</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2015 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2016 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2017 <td id="L315" class="blob-num js-line-number" data-line-number="315"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2018 <td id="LC315" class="blob-code blob-code-inner js-file-line"> transcriptAbundance(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>strain<span class="pl-pds">&#39;</span></span>]]) <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -&gt; ?.cuff/*.*</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2019 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2020 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2021 <td id="L316" class="blob-num js-line-number" data-line-number="316"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2022 <td id="LC316" class="blob-code blob-code-inner js-file-line"> cuff_df <span class="pl-k">=</span> convertToFasta(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>strain<span class="pl-pds">&#39;</span></span>]])</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2023 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2024 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2025 <td id="L317" class="blob-num js-line-number" data-line-number="317"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2026 <td id="LC317" class="blob-code blob-code-inner js-file-line"> countList, weightList <span class="pl-k">=</span> HMMerMotifSearch(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>strain<span class="pl-pds">&#39;</span></span>]], cuff_df)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2027 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2028 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2029 <td id="L318" class="blob-num js-line-number" data-line-number="318"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2030 <td id="LC318" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> relativeFrequencyTable(countList,args[dict[<span class="pl-s"><span class="pl-pds">&#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>]])</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2031 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2032 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2033 <td id="L319" class="blob-num js-line-number" data-line-number="319"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2034 <td id="LC319" class="blob-code blob-code-inner js-file-line"> relWeightList <span class="pl-k">=</span> weightedFrequencyTable(weightList,args[dict[<span class="pl-s"><span class="pl-pds">&#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>]])</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2035 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2036 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2037 <td id="L320" class="blob-num js-line-number" data-line-number="320"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2038 <td id="LC320" class="blob-code blob-code-inner js-file-line"> createStackedBar(args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>]],relWeightList, args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>strain<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>]],args[dict[<span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>]])</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2039 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2040 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2041 <td id="L321" class="blob-num js-line-number" data-line-number="321"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2042 <td id="LC321" 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>]], relFreqList, relWeightList)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2043 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2044 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2045 <td id="L322" class="blob-num js-line-number" data-line-number="322"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2046 <td id="LC322" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2047 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2048 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2049 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2050 <td id="L323" class="blob-num js-line-number" data-line-number="323"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2051 <td id="LC323" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&quot;</span>__main__<span class="pl-pds">&quot;</span></span>:</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2052 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2053 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2054 <td id="L324" class="blob-num js-line-number" data-line-number="324"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2055 <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;Commencing Transcript Mapping&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2056 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2057 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2058 <td id="L325" class="blob-num js-line-number" data-line-number="325"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2059 <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>transcriptMapping(&quot;T_Test&quot;, &quot;Transcripts.1&quot;,&quot;Transcripts.2&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2060 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2061 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2062 <td id="L326" class="blob-num js-line-number" data-line-number="326"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2063 <td id="LC326" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;Processimg Sam Files&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2064 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2065 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2066 <td id="L327" class="blob-num js-line-number" data-line-number="327"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2067 <td id="LC327" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>processSamFiles(&quot;T_Test&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2068 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2069 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2070 <td id="L328" class="blob-num js-line-number" data-line-number="328"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2071 <td id="LC328" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;Assessing Transcript Abundance&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2072 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2073 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2074 <td id="L329" class="blob-num js-line-number" data-line-number="329"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2075 <td id="LC329" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>transcriptAbundance(&quot;T_Test&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2076 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2077 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2078 <td id="L330" class="blob-num js-line-number" data-line-number="330"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2079 <td id="LC330" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print (&quot;Converting to Fasta Subset&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2080 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2081 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2082 <td id="L331" class="blob-num js-line-number" data-line-number="331"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2083 <td id="LC331" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>cuff_df = convertToFasta(&quot;T_Test&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2084 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2085 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2086 <td id="L332" class="blob-num js-line-number" data-line-number="332"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2087 <td id="LC332" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(&quot;Commencing HMMer search&quot;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2088 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2089 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2090 <td id="L333" class="blob-num js-line-number" data-line-number="333"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2091 <td id="LC333" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>countList, weightList = HMMerMotifSearch(&quot;T_Test&quot;,cuff_df)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2092 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2093 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2094 <td id="L334" class="blob-num js-line-number" data-line-number="334"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2095 <td id="LC334" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>relativeFrequencyTable(countList,&#39;T_Test&#39;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2096 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2097 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2098 <td id="L335" class="blob-num js-line-number" data-line-number="335"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2099 <td id="LC335" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>weightedFrequencyTable(weightList,&#39;T_Test&#39;)</span></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2100 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2101 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2102 <td id="L336" class="blob-num js-line-number" data-line-number="336"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2103 <td id="LC336" class="blob-code blob-code-inner js-file-line"> relFreqList <span class="pl-k">=</span> [<span class="pl-c1">0.111842105</span>,<span class="pl-c1">0.059210526</span>,<span class="pl-c1">0.026315789</span>,<span class="pl-c1">0.013157895</span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2104 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2105 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2106 <td id="L337" class="blob-num js-line-number" data-line-number="337"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2107 <td id="LC337" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.006578947</span>,<span class="pl-c1">0.013157895</span>,<span class="pl-c1">0.032894737</span>,<span class="pl-c1">0.019736842</span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2108 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2109 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2110 <td id="L338" class="blob-num js-line-number" data-line-number="338"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2111 <td id="LC338" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.039473684</span>,<span class="pl-c1">0.046052632</span>,<span class="pl-c1">0.217105263</span>,<span class="pl-c1">0.065789474</span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2112 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2113 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2114 <td id="L339" class="blob-num js-line-number" data-line-number="339"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2115 <td id="LC339" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.151315789</span>,<span class="pl-c1">0.059210526</span>,<span class="pl-c1">0.138157895</span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2116 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2117 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2118 <td id="L340" class="blob-num js-line-number" data-line-number="340"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2119 <td id="LC340" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2120 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2121 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2122 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2123 <td id="L341" class="blob-num js-line-number" data-line-number="341"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2124 <td id="LC341" class="blob-code blob-code-inner js-file-line"> relWeightList <span class="pl-k">=</span> [<span class="pl-c1">0.07532571</span>,<span class="pl-c1">0.05900545</span>,<span class="pl-c1">0.009601452</span>,<span class="pl-c1">0.042357532</span>,<span class="pl-c1">0.01236219</span>,<span class="pl-c1">0.001675663</span>,<span class="pl-c1">0.04109726</span>,</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2125 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2126 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2127 <td id="L342" class="blob-num js-line-number" data-line-number="342"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2128 <td id="LC342" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">0.097464248</span>,<span class="pl-c1">0.057491666</span>,<span class="pl-c1">0.05826875</span>,<span class="pl-c1">0.279457473</span>,<span class="pl-c1">0.070004772</span>,<span class="pl-c1">0.065329007</span>,<span class="pl-c1">0.085361298</span>,<span class="pl-c1">0.045197529</span>]</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2129 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2130 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2131 <td id="L343" class="blob-num js-line-number" data-line-number="343"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2132 <td id="LC343" class="blob-code blob-code-inner js-file-line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2133 </td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2134 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2135 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2136 <td id="L344" class="blob-num js-line-number" data-line-number="344"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2137 <td id="LC344" class="blob-code blob-code-inner js-file-line"> createStackedBar(<span class="pl-s"><span class="pl-pds">&#39;</span>T_Test<span class="pl-pds">&#39;</span></span>,relWeightList, <span class="pl-s"><span class="pl-pds">&#39;</span>Tc148<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>PDF_Yes<span class="pl-pds">&#39;</span></span>,<span class="pl-s"><span class="pl-pds">&#39;</span>results<span class="pl-pds">&#39;</span></span>)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2138 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2139 <tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2140 <td id="L345" class="blob-num js-line-number" data-line-number="345"></td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2141 <td id="LC345" class="blob-code blob-code-inner js-file-line"> createHTML(<span class="pl-s"><span class="pl-pds">&quot;</span>t_test<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>results/t_test.html<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>results<span class="pl-pds">&quot;</span></span>,relFreqList,relWeightList)</td>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2142 </tr>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2143 </table>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2144
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2145 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2146 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2147 <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2148 </summary>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2149 <details-menu>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2150 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2151 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2152 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2153 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/johnheap/VAPPER-Galaxy/blame/a4e16d71fe985f389930c02f94354b87d3aabadb/Tryp_T.py">View git blame</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2154 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/johnheap/VAPPER-Galaxy/issues/new">Reference in new issue</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2155 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2156 </details-menu>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2157 </details>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2158
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2159 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2160
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2161 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2162
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2163
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2164
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2165 <details class="details-reset details-overlay details-overlay-dark">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2166 <summary data-hotkey="l" aria-label="Jump to line"></summary>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2167 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2168 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="&#x2713;" />
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2169 <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line&hellip;" aria-label="Jump to line" autofocus>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2170 <button type="submit" class="btn" data-close-dialog>Go</button>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2171 </form> </details-dialog>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2172 </details>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2173
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2174
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2175
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2176 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2177 <div class="modal-backdrop js-touch-events"></div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2178 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2179
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2180 </main>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2181 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2182
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2183
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2184 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2185
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2186
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2187 <div class="footer container-lg width-full p-responsive" role="contentinfo">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2188 <div class="position-relative d-flex flex-row-reverse flex-lg-row flex-wrap flex-lg-nowrap flex-justify-center flex-lg-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light ">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2189 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2190 <li class="mr-3 mr-lg-0">&copy; 2019 <span title="0.38259s from unicorn-7478f9985c-skxnd">GitHub</span>, Inc.</li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2191 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2192 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2193 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to security, text:security" href="https://github.com/security">Security</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2194 <li class="mr-3 mr-lg-0"><a href="https://githubstatus.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2195 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2196 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2197
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2198 <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2199 <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2200 </a>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2201 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2202 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2203 <li class="mr-3 mr-lg-0"><a href="https://github.com/pricing" data-ga-click="Footer, go to Pricing, text:Pricing">Pricing</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2204 <li class="mr-3 mr-lg-0"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2205 <li class="mr-3 mr-lg-0"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2206 <li class="mr-3 mr-lg-0"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2207 <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2208
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2209 </ul>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2210 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2211 <div class="d-flex flex-justify-center pb-6">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2212 <span class="f6 text-gray-light"></span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2213 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2214 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2215
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2216
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2217
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2218 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2219 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2220 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2221 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2222 </button>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2223 You can’t perform that action at this time.
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2224 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2225
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2226
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2227 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2228 <script crossorigin="anonymous" integrity="sha512-oFBEYscCdWEyvUQehaYyaCSiKtIN4UvpfFHNpIXLUTSQ35JcacPNj86R8fgJfI1e7BOjbLZPTv1nJg3TECiMLw==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-7af24171.js"></script>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2229
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2230 <script crossorigin="anonymous" async="async" integrity="sha512-b9BDH7EZq1yaR2fUH08I378zVkToScLiQ//L0gdyPviliuwpWiVFkB8uW0K8zZszdeLeBpib7wGBLkPiIFgyHg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-2a8c2b54.js"></script>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2231
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2232
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2233
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2234 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2235 >
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2236 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2237 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2238 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2239 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2240 <template id="site-details-dialog">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2241 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2242 <summary role="button" aria-label="Close dialog"></summary>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2243 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2244 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2245 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2246 </button>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2247 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2248 </details-dialog>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2249 </details>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2250 </template>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2251
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2252 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2253 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2254 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2255 </div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2256
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2257 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2258
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2259 </body>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2260 </html>
25226d33642e Uploaded
johnheap
parents: 4
diff changeset
2261