Mercurial > repos > iuc > jbrowse
diff jbrowse.py @ 0:2c9e5136b416 draft
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 |
| parents | |
| children | 497c6bb3b717 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse.py Mon May 04 17:21:38 2015 -0400 @@ -0,0 +1,59 @@ +#!/usr/bin/env python +import os +import shutil +import argparse +import subprocess +import hashlib + +TN_TABLE = { + 'gff3': '--gff', + 'gff': '--gff', + 'bed': '--bed', + # 'genbank': '--gbk', +} + + +def process_genome(jbrowse_dir, genome): + subprocess.check_output(['perl', 'bin/prepare-refseqs.pl', '--fasta', genome], cwd=jbrowse_dir) + + +def process_annotations(jbrowse_dir, annot_file, annot_label, annot_format, + **kwargs): + key = hashlib.md5(annot_file).hexdigest() + + cmd = ['perl', 'bin/flatfile-to-json.pl', TN_TABLE.get(annot_format, 'gff'), + annot_file, '--trackLabel', key, '--key', annot_label] + subprocess.check_output(cmd, cwd=jbrowse_dir) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description="", epilog="") + parser.add_argument('genome', type=file, help='Input genome file') + + parser.add_argument('--gff3', type=file, nargs='*', help='GFF3/BED/GBK File') + parser.add_argument('--gff3_format', choices=['gff3', 'gff', 'bed', 'gbk'], nargs='*', help='GFF3/BED/GBK Format') + parser.add_argument('--gff3_label', type=str, nargs='*', help='GFF3/BED/GBK Label') + + parser.add_argument('--jbrowse', help='Folder containing a jbrowse release') + parser.add_argument('--outdir', help='Output directory', default='out') + args = parser.parse_args() + + jbrowse_dir = os.path.join(args.outdir, 'JBrowse-1.11.6') + shutil.copytree(args.jbrowse, jbrowse_dir) + + process_genome(jbrowse_dir, os.path.realpath(args.genome.name)) + + for gff3, gff3_format, gff3_label in zip(args.gff3, args.gff3_format, args.gff3_label): + gff3_path = os.path.realpath(gff3.name) + process_annotations(jbrowse_dir, gff3_path, gff3_label, gff3_format) + + print """ + <html> + <body> + <script type="text/javascript"> + window.location=JBrowse-1.11.6/index.html + </script> + <a href="JBrowse-1.11.6/index.html">Go to JBrowse</a> + </body> + </html> + """