Mercurial > repos > xuebing > sharplabtool

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