Mercurial > repos > devteam > count_gff_features

comparison count_gff_features.py @ 1:188392a0d0a8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
author devteam
date Tue, 06 Jun 2017 18:37:53 -0400
parents fabda887a71f
children
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0:fabda887a71f 1:188392a0d0a8
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 # This tool takes a gff file as input and counts the number of features in it. 2 # This tool takes a gff file as input and counts the number of features in it.
3 3
4 import sys, fileinput 4 from __future__ import print_function
5 from galaxy import eggs 5
6 import fileinput
7 import sys
8
9 from bx.intervals.io import GenomicInterval
6 from galaxy.datatypes.util.gff_util import GFFReaderWrapper 10 from galaxy.datatypes.util.gff_util import GFFReaderWrapper
7 from bx.intervals.io import GenomicInterval
8 11
9 # Get args. 12 # Get args.
10 input_file = sys.argv[1:] 13 input_file = sys.argv[1:]
11 14
12 # Count features. 15 # Count features.
13 count = 0 16 count = 0
14 for feature in GFFReaderWrapper( fileinput.FileInput( input_file ), fix_strand=True ): 17 for feature in GFFReaderWrapper( fileinput.FileInput( input_file ), fix_strand=True ):
15 if isinstance( feature, GenomicInterval ): 18 if isinstance( feature, GenomicInterval ):
16 count += 1 19 count += 1
17 20
18 print count 21 print(count)