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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 18:37:39 -0400
parents 002a1e6ef8d9
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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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115bba486116 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
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4 from __future__ import print_function
115bba486116 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
devteam
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115bba486116 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
devteam
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6 import fileinput
115bba486116 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
devteam
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7 import sys
115bba486116 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
devteam
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115bba486116 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
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9 from bx.intervals.io import GenomicInterval
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10 from galaxy.datatypes.util.gff_util import GFFReaderWrapper
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11
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12 # Get args.
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13 input_file = sys.argv[1:]
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14
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15 # Count features.
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16 count = 0
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17 for feature in GFFReaderWrapper( fileinput.FileInput( input_file ), fix_strand=True ):
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18 if isinstance( feature, GenomicInterval ):
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19 count += 1
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115bba486116 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
devteam
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21 print(count)