Mercurial > repos > jvolkening > nanopore_qc

comparison yaml_to_html.pl @ 0:e0006d8bf849 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
author jvolkening
date Sat, 02 Mar 2024 03:35:34 +0000
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-1:000000000000 0:e0006d8bf849
1 #!/usr/bin/env perl
2
3 use strict;
4 use warnings;
5 use 5.012;
6
7 use YAML::XS qw/LoadFile/;
8 use MIME::Base64;
9 use autodie;
10
11 my ($fn_yaml, $dir_in, $fn_out) = @ARGV;
12
13 die "Can't find or read input file: $!\n"
14 if (! -r $fn_yaml);
15
16 # set output filehandle based on arguments
17 my $fh = \*STDOUT;
18 if (defined $fn_out) {
19 open $fh, '>', $fn_out;
20 }
21
22 my $yaml = LoadFile($fn_yaml);
23
24 convert($yaml, $dir_in);
25
26 sub convert {
27
28 my ($yaml) = @_;
29
30 print {$fh} header();
31
32 say {$fh} " <h3>Summary statistics</h3>";
33
34 for my $grp (sort keys %$yaml) {
35
36 my $ref = $yaml->{$grp};
37
38 next if (! ref $ref);
39 next if (! defined $ref->{'total.gigabases'});
40
41 print {$fh} <<"CONTENT"
42 <table>
43 <caption>$grp</caption>
44 <tr>
45 <td>Total Yield (Gb)</td>
46 <td>$ref->{'total.gigabases'}</td>
47 </tr>
48 <tr>
49 <td>Total Reads</td>
50 <td>$ref->{'total.reads'}</td>
51 </tr>
52 <tr>
53 <td>Mean Length</td>
54 <td>$ref->{'mean.length'}</td>
55 </tr>
56 <tr>
57 <td>Median Length</td>
58 <td>$ref->{'median.length'}</td>
59 </tr>
60 <tr>
61 <td>Max Length</td>
62 <td>$ref->{'max.length'}</td>
63 </tr>
64 <tr>
65 <td>Mean Q</td>
66 <td>$ref->{'mean.q'}</td>
67 </tr>
68 <tr>
69 <td>Median Q</td>
70 <td>$ref->{'median.q'}</td>
71 </tr>
72 </table>
73 CONTENT
74
75 }
76
77 my %figs = (
78 'length_histogram' => "Read length distribution",
79 'q_histogram' => "Mean quality score distribution",
80 'reads_per_hour' => "Yield over time",
81 'cumulative_yield' => "Cumulative yield over time",
82 'yield_summary' => "Yield by read length cutoff",
83 'flowcell_overview' => "Median read quality per channel",
84 'length_by_hour' => "Read length over time",
85 'q_by_hour' => "Read quality over time",
86 'length_vs_q' => "Read length vs. quality",
87 );
88
89 my @order = qw/
90 length_histogram
91 q_histogram
92 reads_per_hour
93 cumulative_yield
94 yield_summary
95 flowcell_overview
96 length_by_hour
97 q_by_hour
98 length_vs_q
99 /;
100
101
102 say {$fh} " <h3>QC plots</h3>";
103 say {$fh} " <p>(Click on plot for high-resolution version, or in Chrome \"Open link in new tab\")</p>";
104
105 for my $base (@order) {
106
107 my $caption = $figs{$base} // die "No caption found for $base";
108
109 # Base64-encode images
110 my $fn_img_full = "$dir_in/$base.png";
111 my $fn_img_screen = "$dir_in/$base.screen.png";
112 die "Failed to find or read $fn_img_full"
113 if (! -r $fn_img_full);
114 die "Failed to find or read $fn_img_screen"
115 if (! -r $fn_img_screen);
116 my $img_full = encode($fn_img_full);
117 my $img_screen = encode($fn_img_screen);
118
119 print {$fh} <<"CONTENT"
120 <a href="data:image/png;base64,$img_full">
121 <figure>
122 <img src="data:image/png;base64,$img_screen" alt="$base" />
123 <figcaption>$caption</figcaption>
124 </figure>
125 </a>
126 CONTENT
127
128 }
129
130 print {$fh} footer();
131
132 }
133
134 sub encode {
135
136 my ($fn) = @_;
137 open my $in, '<:raw', $fn;
138 local($/) = undef;
139 return encode_base64(<$in>);
140
141 }
142
143 sub header {
144
145 return <<'HEADER';
146 <?xml version="1.0" encoding="utf-8"?>
147 <!DOCTYPE html>
148 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
149 <head>
150 <title></title>
151 <meta http-equiv="content-type" content="application/xhtml+xml; charset=utf-8" />
152 <style>
153 h2 {
154 padding: 0.3em;
155 background-color: #000000;
156 color: #ffffff;
157 margin: 1em 0 2em 0;
158 }
159 h3 {
160 padding: 0em 0.2em 0em 0.2em;
161 color: #555555;
162 border: solid 1px black;
163 border-width: 0px 0px 1px 0px;
164 margin: 2em 0 0.4em 0;
165 }
166 tr {
167 margin: 0;
168 }
169 tr:nth-child(even) {
170 background-color: #bbbbbb;
171 }
172 tr:nth-child(odd) {
173 background-color: #eeeeee;
174 }
175 caption {
176 text-align: left;
177 font-weight: bold;
178 background-color: #550000;
179 color: #ffffff;
180 padding: 0.1em 0.2em;
181 }
182 table {
183 margin: 1em;
184 padding: 0.3em;
185 }
186 td {
187 margin: 0;
188 padding: 0 0.4em;
189 }
190 tr td:nth-child(1) {
191 color: #550000;
192 }
193 figure {
194 display: table;
195 margin: 2em 0;
196 }
197 figcaption {
198 display: table-caption;
199 caption-side: top;
200 font-size: 1.1em;
201 text-decoration: none;
202 text-align: center;
203 font-weight: bold;
204 background-color: #550000;
205 color: #ffffff;
206 padding: 0.1em 0.2em;
207 margin: 2em 0 0.7em 0;
208 }
209
210 </style>
211 </head>
212 <body>
213
214 <h2>NanoporeQC Report</h2>
215 HEADER
216
217 }
218
219 sub footer {
220
221 return <<'FOOTER';
222
223 </body>
224 </html>
225 FOOTER
226
227 }