Mercurial > repos > xuebing > sharplabtool

comparison tools/stats/count_gff_features.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2 # This tool takes a gff file as input and counts the number of features in it.
3
4 import sys, fileinput
5 from galaxy import eggs
6 from galaxy.datatypes.util.gff_util import GFFReaderWrapper
7 from bx.intervals.io import GenomicInterval
8
9 # Get args.
10 input_file = sys.argv[1:]
11
12 # Count features.
13 count = 0
14 for feature in GFFReaderWrapper( fileinput.FileInput( input_file ), fix_strand=True ):
15 if isinstance( feature, GenomicInterval ):
16 count += 1
17
18 print count