Mercurial > repos > devteam > count_gff_features

comparison count_gff_features.py @ 0:fabda887a71f draft

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Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:56:10 -0400
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children 188392a0d0a8
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-1:000000000000 0:fabda887a71f
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