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comparison gops_coverage.py @ 3:4ef9819dc7fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:41:02 -0400
parents bc9c66c1e9c9
children
comparison
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2:bc9c66c1e9c9 3:4ef9819dc7fb
5 5
6 usage: %prog bed_file_1 bed_file_2 out_file 6 usage: %prog bed_file_1 bed_file_2 out_file
7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file 7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file 8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
9 """ 9 """
10 from __future__ import print_function
11
10 import fileinput 12 import fileinput
11 import sys 13 import sys
14
15 from bx.cookbook import doc_optparse
12 from bx.intervals.io import GenomicInterval, NiceReaderWrapper 16 from bx.intervals.io import GenomicInterval, NiceReaderWrapper
13 from bx.intervals.operations.coverage import coverage 17 from bx.intervals.operations.coverage import coverage
14 from bx.cookbook import doc_optparse
15 from bx.tabular.io import ParseError 18 from bx.tabular.io import ParseError
16 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped 19 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
17 20
18 assert sys.version_info[:2] >= ( 2, 4 ) 21 assert sys.version_info[:2] >= ( 2, 4 )
19 22
46 for line in coverage( [g1, g2] ): 49 for line in coverage( [g1, g2] ):
47 if type( line ) is GenomicInterval: 50 if type( line ) is GenomicInterval:
48 out_file.write( "%s\n" % "\t".join( line.fields ) ) 51 out_file.write( "%s\n" % "\t".join( line.fields ) )
49 else: 52 else:
50 out_file.write( "%s\n" % line ) 53 out_file.write( "%s\n" % line )
51 except ParseError, exc: 54 except ParseError as exc:
52 out_file.close() 55 out_file.close()
53 fail( "Invalid file format: %s" % str( exc ) ) 56 fail( "Invalid file format: %s" % str( exc ) )
54 57
55 out_file.close() 58 out_file.close()
56 59
57 if g1.skipped > 0: 60 if g1.skipped > 0:
58 print skipped( g1, filedesc=" of 1st dataset" ) 61 print(skipped( g1, filedesc=" of 1st dataset" ))
59 if g2.skipped > 0: 62 if g2.skipped > 0:
60 print skipped( g2, filedesc=" of 2nd dataset" ) 63 print(skipped( g2, filedesc=" of 2nd dataset" ))
64
61 65
62 if __name__ == "__main__": 66 if __name__ == "__main__":
63 main() 67 main()