Mercurial > repos > iuc > jbrowse

comparison jbrowse.py @ 0:2c9e5136b416 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
author iuc
date Mon, 04 May 2015 17:21:38 -0400
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children 497c6bb3b717
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-1:000000000000 0:2c9e5136b416
1 #!/usr/bin/env python
2 import os
3 import shutil
4 import argparse
5 import subprocess
6 import hashlib
7
8 TN_TABLE = {
9 'gff3': '--gff',
10 'gff': '--gff',
11 'bed': '--bed',
12 # 'genbank': '--gbk',
13 }
14
15
16 def process_genome(jbrowse_dir, genome):
17 subprocess.check_output(['perl', 'bin/prepare-refseqs.pl', '--fasta', genome], cwd=jbrowse_dir)
18
19
20 def process_annotations(jbrowse_dir, annot_file, annot_label, annot_format,
21 **kwargs):
22 key = hashlib.md5(annot_file).hexdigest()
23
24 cmd = ['perl', 'bin/flatfile-to-json.pl', TN_TABLE.get(annot_format, 'gff'),
25 annot_file, '--trackLabel', key, '--key', annot_label]
26 subprocess.check_output(cmd, cwd=jbrowse_dir)
27
28
29 if __name__ == '__main__':
30 parser = argparse.ArgumentParser(description="", epilog="")
31 parser.add_argument('genome', type=file, help='Input genome file')
32
33 parser.add_argument('--gff3', type=file, nargs='*', help='GFF3/BED/GBK File')
34 parser.add_argument('--gff3_format', choices=['gff3', 'gff', 'bed', 'gbk'], nargs='*', help='GFF3/BED/GBK Format')
35 parser.add_argument('--gff3_label', type=str, nargs='*', help='GFF3/BED/GBK Label')
36
37 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
38 parser.add_argument('--outdir', help='Output directory', default='out')
39 args = parser.parse_args()
40
41 jbrowse_dir = os.path.join(args.outdir, 'JBrowse-1.11.6')
42 shutil.copytree(args.jbrowse, jbrowse_dir)
43
44 process_genome(jbrowse_dir, os.path.realpath(args.genome.name))
45
46 for gff3, gff3_format, gff3_label in zip(args.gff3, args.gff3_format, args.gff3_label):
47 gff3_path = os.path.realpath(gff3.name)
48 process_annotations(jbrowse_dir, gff3_path, gff3_label, gff3_format)
49
50 print """
51 <html>
52 <body>
53 <script type="text/javascript">
54 window.location=JBrowse-1.11.6/index.html
55 </script>
56 <a href="JBrowse-1.11.6/index.html">Go to JBrowse</a>
57 </body>
58 </html>
59 """