parses annotations from GenBank files

Author: chrisgulvik

Diff for: extract.nfo.from.GBK.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+
+
+# Example: <script>.py -i input.gbk -s VFDB_setA_pro -f CDS -q inference -r product
+from argparse import ArgumentParser
+from Bio import SeqIO
+
+def parseArgs():
+	parser = ArgumentParser(description='Parses a GenBank file for data '
+		'given a search term and specified fields to query. An additional '
+		'parsed field is also reported in tab-delimited format.', add_help=False)
+	req = parser.add_argument_group('Required')
+	req.add_argument('-i', '--infile', required=True, metavar='FILE',
+		help='input GenBank file')
+	req.add_argument('-s', '--query-search', required=True, metavar='STR',
+		type=str, help='search term to look for within the query feature '
+		'and query qualifier')
+	opt = parser.add_argument_group('Optional')
+	opt.add_argument('-f', '--query-feature', default='CDS', metavar='STR',
+		help='genbank feature type to search in, e.g., CDS, gene, rRNA, '
+		'source, tRNA, misc_feature')
+	opt.add_argument('-h', '--help', action='help',
+		help='show this help message and exit')
+	opt.add_argument('-o', '--outfile', default='parsed.tab', metavar='FILE',
+		help='output tab-delimited file containing <locus_tag>\\t'
+		'<query-qualifier>\\t<report-qualifier>  [./parsed.tab]')
+	opt.add_argument('-q', '--query-qualifier', default='inference',
+		metavar='STR', help='qualifier term within each genbank feature to '
+		'search in, e.g., locus_tag, inference, codon_start, product, '
+		'transl_table, translation')
+	opt.add_argument('-r', '--report-qualifier', default='product',
+		metavar='STR', help='additional qualifier term to parse data from '
+		'and report when queries are found')
+	return parser.parse_args()
+
+def main():
+	opts = parseArgs()
+	gbk          = opts.infile
+	query_feat   = opts.query_feature
+	query_qualif = opts.query_qualifier
+	query_str    = opts.query_search
+	rep_qualif   = opts.report_qualifier
+	outfile      = opts.outfile
+
+	l = []
+	for rec in SeqIO.parse(open(gbk, 'r'), 'genbank'):
+		for feature in rec.features:
+			if query_feat == feature.type and \
+			query_qualif in feature.qualifiers:
+				list_to_search_against = feature.qualifiers[query_qualif]
+				found = [s for s in list_to_search_against if query_str in s]
+				if len(found) > 0:
+					hit = ' '.join(found)
+					l.append('{}\t{}\t{}'.format(
+						feature.qualifiers['locus_tag'][0], hit,
+						''.join(feature.qualifiers[rep_qualif][0])))
+
+	with open(opts.outfile, 'w') as ofh:
+		for i in l:
+			ofh.write('{}\n'.format(i))
+
+if __name__ == '__main__':
+	main()