Mercurial > repos > jjohnson > gffutils
comparison create_gffdb.py @ 0:8ba71aead5bc draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
| author | jjohnson |
|---|---|
| date | Sun, 08 Apr 2018 13:26:47 -0400 |
| parents | |
| children | 8880c2e4b2ee |
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| -1:000000000000 | 0:8ba71aead5bc |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 from __future__ import print_function | |
| 4 | |
| 5 import argparse | |
| 6 import json | |
| 7 import sys | |
| 8 | |
| 9 import gffutils | |
| 10 | |
| 11 | |
| 12 def __main__(): | |
| 13 parser = argparse.ArgumentParser( | |
| 14 description='Convert mga output to bed and tsv') | |
| 15 parser.add_argument( | |
| 16 'input_gff', | |
| 17 help="gff3 or gtf file to load") | |
| 18 parser.add_argument( | |
| 19 'gff_sqlite', | |
| 20 help="sqlite file") | |
| 21 args = parser.parse_args() | |
| 22 | |
| 23 db = gffutils.create_db(args.input_gff, args.gff_sqlite) | |
| 24 version = db.execute('SELECT version FROM meta').fetchone()[0] | |
| 25 print('version:%s' % version,file=sys.stdout) | |
| 26 dialect = db.execute('SELECT dialect FROM meta').fetchone()[0] | |
| 27 info = json.loads(dialect) | |
| 28 if 'fmt' in info: | |
| 29 print('format:%s' % info['fmt'],file=sys.stdout) | |
| 30 seqids = [r[0] for r in db.execute('SELECT distinct seqid FROM features').fetchall()] | |
| 31 print('seqids:%s' % ','.join(seqids),file=sys.stdout) | |
| 32 | |
| 33 | |
| 34 if __name__ == "__main__": | |
| 35 __main__() |