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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
author iuc
date Sun, 03 Jan 2021 14:58:02 +0000
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-1:000000000000 0:1b52f0c8ad7f
1 <!doctype html>
2 <html lang="en">
3 <head>
4 <meta charset="utf-8" />
5 <title>ParsEval Summary</title>
6 <link rel="stylesheet" type="text/css" href="parseval.css" />
7 <script type="text/javascript" language="javascript" src="vendor/jquery.js"></script>
8 <script type="text/javascript" language="javascript" src="vendor/jquery.dataTables.js"></script>
9 <script type="text/javascript">
10 $(document).ready(function() {
11 $('#seqlist').dataTable( {
12 "sScrollY": "400px",
13 "bPaginate": false,
14 "bScrollCollapse": true,
15 "bSort": false,
16 "bFilter": false,
17 "bInfo": false
18 });
19 } );
20 </script>
21 </head>
22 <body>
23 <div id="content">
24 <h1>ParsEval Summary</h1>
25 <pre class="command">
26 Started: 03 Jan 2021, 02:54PM
27 Reference annotations: /tmp/tmpok6hen4l/files/7/2/c/dataset_72c6fa9a-e400-4213-a1ef-ac6fc6ab18e7.dat
28 Prediction annotations: /tmp/tmpok6hen4l/files/d/2/0/dataset_d20b7bb7-e832-4eb2-917e-7b76fdb1a0cb.dat
29 Executing command: parseval --delta 0 --maxtrans 32 -w -f html -o /tmp/tmpok6hen4l/job_working_directory/000/43/working/dataset_63abed3a-aaab-41d9-b66b-4030368d9362_files /tmp/tmpok6hen4l/files/7/2/c/dataset_72c6fa9a-e400-4213-a1ef-ac6fc6ab18e7.dat /tmp/tmpok6hen4l/files/d/2/0/dataset_d20b7bb7-e832-4eb2-917e-7b76fdb1a0cb.dat </pre>
30
31 <h2>Sequences compared</h2>
32 <p class="indent">Click on a sequence ID below to see comparison results for individual loci.</p>
33 <table id="seqlist" class="indent">
34 <thead>
35 <tr>
36 <th>Sequence</th>
37 <th>Refr genes</th>
38 <th>Pred genes</th>
39 <th>Loci</th>
40 </tr>
41 </thead>
42 <tbody>
43 <tr><td><a href="Chr1/index.html">Chr1</a></td><td>4</td><td>4</td><td>4</td></tr>
44 </tbody>
45 </table>
46
47 <h2>Gene loci <span class="tooltip">[?]<span class="tooltip_text">If a gene annotation overlaps with another gene annotation, those annotations are associated with the same gene locus. See <a target="_blank" href="http://aegean.readthedocs.io/en/latest/loci.html">this page</a> for a formal definition of a locus annotation.</span></span></h2>
48 <table class="table_normal">
49 <tr><td>shared</td><td>4</td></tr>
50 <tr><td>unique to reference</td><td>0</td></tr>
51 <tr><td>unique to prediction</td><td>0</td></tr>
52 <tr><th class="right-align">Total</th><td>4</td></tr>
53 </table>
54
55 <h2>Reference annotations</h2>
56 <table class="table_normal">
57 <tr><td>genes</td><td>4</td></tr>
58 <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.000</td></tr>
59 <tr><td>transcripts</td><td>5</td></tr>
60 <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.250</td></tr>
61 <tr class="cell_small"><td class="cell_indent">average per gene</td><td>1.250</td></tr>
62 </table>
63
64 <h2>Prediction annotations</h2>
65 <table class="table_normal">
66 <tr><td>genes</td><td>4</td></tr>
67 <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.000</td></tr>
68 <tr><td>transcripts</td><td>5</td></tr>
69 <tr class="cell_small"><td class="cell_indent">average per locus</td><td>1.250</td></tr>
70 <tr class="cell_small"><td class="cell_indent">average per gene</td><td>1.250</td></tr>
71 </table>
72
73 <h2>Comparisons</h2>
74 <table class="comparisons">
75 <tr><th>Total comparisons</th><th>5</th></tr>
76 <tr><td><a href="perfectmatches.html">(+)</a> perfect matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Prediction transcripts (exons, coding sequences, and UTRs) line up perfectly with reference transcripts.</span></span></td><td>5 (100.0%)</tr>
77 <tr class="cell_small"><td class="cell_indent">average length</td><td>3607.40 bp</td></tr>
78 <tr class="cell_small"><td class="cell_indent">average # refr exons</td><td>7.60</td></tr>
79 <tr class="cell_small"><td class="cell_indent">average # pred exons</td><td>7.60</td></tr>
80 <tr class="cell_small"><td class="cell_indent">average refr CDS length</td><td>449.40 aa</td></tr>
81 <tr class="cell_small"><td class="cell_indent">average pred CDS length</td><td>449.40 aa</td></tr>
82 <tr><td>(+) perfect matches with mislabeled UTRs <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">5'/3' orientation of UTRs is reversed between reference and prediction, but a perfect match in all other aspects.</span></span></td><td>0 (0.0%)</tr>
83 <tr><td>(+) CDS structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match, but prediction coding sequence(s) line up perfectly with reference coding sequence(s).</span></span></td><td>0 (0.0%)</tr>
84 <tr><td>(+) exon structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match or CDS match, but prediction exon structure is identical to reference exon structure.</span></span></td><td>0 (0.0%)</tr>
85 <tr><td>(+) UTR structure matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Not a perfect match, CDS match, or exon structure match, but prediction UTRs line up perfectly with reference UTRs.</span></span></td><td>0 (0.0%)</tr>
86 <tr><td>(+) non-matches <span class="tooltip"><span class="small_tooltip">[?]</span><span class="tooltip_text">Differences in CDS, exon, and UTR structure.</span></span></td><td>0 (0.0%)</tr>
87 </table>
88
89 <h3>CDS structure comparison</h3>
90 <table class="table_normal table_extra_indent">
91 <tr><td>reference CDS segments</td><td>35</td></tr>
92 <tr class="cell_small"><td class="cell_indent">match prediction</td><td>35 (100.0%)</td></tr>
93 <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
94 <tr><td>prediction CDS segments</td><td>35</td></tr>
95 <tr class="cell_small"><td class="cell_indent">match prediction</td><td>35 (100.0%)</td></tr>
96 <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
97 <tr><td>Sensitivity</td><td>1.000</td></tr>
98 <tr><td>Specificity</td><td>1.000</td></tr>
99 <tr><td>F1 score</td><td>1.000</td></tr>
100 <tr><td>Annotation edit distance</td><td>0.000</td></tr>
101 </table>
102
103 <h3>Exon structure comparison</h3>
104 <table class="table_normal table_extra_indent">
105 <tr><td>reference exons</td><td>38</td></tr>
106 <tr class="cell_small"><td class="cell_indent">match prediction</td><td>38 (100.0%)</td></tr>
107 <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
108 <tr><td>prediction exons</td><td>38</td></tr>
109 <tr class="cell_small"><td class="cell_indent">match prediction</td><td>38 (100.0%)</td></tr>
110 <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
111 <tr><td>Sensitivity</td><td>1.000</td></tr>
112 <tr><td>Specificity</td><td>1.000</td></tr>
113 <tr><td>F1 score</td><td>1.000</td></tr>
114 <tr><td>Annotation edit distance</td><td>0.000</td></tr>
115 </table>
116
117 <h3>UTR structure comparison</h3>
118 <table class="table_normal table_extra_indent">
119 <tr><td>reference UTR segments</td><td>12</td></tr>
120 <tr class="cell_small"><td class="cell_indent">match prediction</td><td>12 (100.0%)</td></tr>
121 <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
122 <tr><td>prediction UTR segments</td><td>12</td></tr>
123 <tr class="cell_small"><td class="cell_indent">match prediction</td><td>12 (100.0%)</td></tr>
124 <tr class="cell_small"><td class="cell_indent">don't match prediction</td><td>0 (0.0%)</td></tr>
125 <tr><td>Sensitivity</td><td>1.000</td></tr>
126 <tr><td>Specificity</td><td>1.000</td></tr>
127 <tr><td>F1 score</td><td>1.000</td></tr>
128 <tr><td>Annotation edit distance</td><td>0.000</td></tr>
129 </table>
130
131 <h3>Nucleotide-level comparison</h3>
132 <table class="table_wide table_extra_indent">
133 <tr><th>&nbsp;</th><th>CDS</th><th>UTRs</th><th>Overall</th></tr>
134 <tr><th class="left-align">matching coefficient</th><td>1.000</td><td>1.000</td><td>1.000</td></tr>
135 <tr><th class="left-align">correlation coefficient</th><td>1.000</td><td>1.000</td><td>--</td></tr>
136 <tr><th class="left-align">sensitivity</th><td>1.000</td><td>1.000</td><td>--</td></tr>
137 <tr><th class="left-align">specificity</th><td>1.000</td><td>1.000</td><td>--</td></tr>
138 <tr><th class="left-align">F1 score</th><td>1.000</td><td>1.000</td><td>--</td></tr>
139 <tr><th class="left-align">annotation edit distance</th><td>0.000</td><td>0.000</td><td>--</td></tr>
140 </table>
141
142 <p class="footer">
143 Generated by <a href="https://github.com/standage/AEGeAn/releases/tag/v0.16.0">AEGeAn v0.16.0 (stable )</a>.<br />
144 Copyright © 2016 <a href="http://aegean.readthedocs.io/en/latest/contrib.html">AEGeAn authors</a>.<br />
145 See <a href="LICENSE">LICENSE</a> for details. </p>
146 </div> </body> </html>