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annotate create_gffdb.py @ 2:b956465b8893 draft default tip

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit f84d4d6e7fa7617e4b8298007db22e1355071213-dirty
author jjohnson
date Tue, 17 Apr 2018 10:19:30 -0400
parents 8880c2e4b2ee
children
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1 #!/usr/bin/env python
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3 from __future__ import print_function
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5 import argparse
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6 import json
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7 import sys
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9 import gffutils
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12 def __main__():
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13 parser = argparse.ArgumentParser(
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14 description='Convert mga output to bed and tsv')
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15 parser.add_argument(
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16 'input_gff',
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17 help="gff3 or gtf file to load")
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18 parser.add_argument(
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19 'gff_sqlite',
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20 help="sqlite file")
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21 parser.add_argument(
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22 '--create_introns',
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23 action='store_true',
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24 help='')
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25 parser.add_argument(
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26 '--disable_infer_transcripts',
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27 action='store_true',
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28 help='')
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29 parser.add_argument(
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30 '--disable_infer_genes',
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31 action='store_true',
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32 help='')
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33 parser.add_argument(
8880c2e4b2ee planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
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34 '-v', '--verbose', action='store_true', help='Verbose')
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35 args = parser.parse_args()
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36
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37 db = gffutils.create_db(
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38 args.input_gff, args.gff_sqlite,
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39 disable_infer_transcripts=args.disable_infer_transcripts,
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40 disable_infer_genes=args.disable_infer_genes)
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41 version = db.execute('SELECT version FROM meta').fetchone()[0]
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42 print('version:%s' % version, file=sys.stdout)
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43 dialect = db.execute('SELECT dialect FROM meta').fetchone()[0]
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44 if args.create_introns:
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45 db.create_introns()
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46 info = json.loads(dialect)
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47 if 'fmt' in info:
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48 print('format:%s' % info['fmt'], file=sys.stdout)
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49 seqids = [r[0] for r in
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50 db.execute('SELECT distinct seqid FROM features').fetchall()]
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51 print('seqids:%s' % ','.join(seqids), file=sys.stdout)
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52
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53
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54 if __name__ == "__main__":
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55 __main__()