Mercurial > repos > devteam > complement

comparison gops_complement.py @ 4:38c8bb402872 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:40:33 -0400
parents e0a23ab32d7f
children
comparison
equal deleted inserted replaced
3:e0a23ab32d7f 4:38c8bb402872
5 usage: %prog in_file out_file 5 usage: %prog in_file out_file
6 -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file 6 -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
7 -l, --lengths=N: Filename of .len file for species (chromosome lengths) 7 -l, --lengths=N: Filename of .len file for species (chromosome lengths)
8 -a, --all: Complement all chromosomes (Genome-wide complement) 8 -a, --all: Complement all chromosomes (Genome-wide complement)
9 """ 9 """
10 from __future__ import print_function
10 11
12 import fileinput
11 import sys 13 import sys
12 import fileinput 14
15 from bx.cookbook import doc_optparse
13 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper 16 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper
14 from bx.intervals.operations.complement import complement 17 from bx.intervals.operations.complement import complement
15 from bx.intervals.operations.subtract import subtract 18 from bx.intervals.operations.subtract import subtract
16 from bx.cookbook import doc_optparse
17 from bx.tabular.io import ParseError 19 from bx.tabular.io import ParseError
18 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped 20 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
19 21
20 assert sys.version_info[:2] >= ( 2, 4 ) 22 assert sys.version_info[:2] >= ( 2, 4 )
21 23
81 for interval in generator: 83 for interval in generator:
82 if type( interval ) is GenomicInterval: 84 if type( interval ) is GenomicInterval:
83 out_file.write( "%s\n" % "\t".join( interval ) ) 85 out_file.write( "%s\n" % "\t".join( interval ) )
84 else: 86 else:
85 out_file.write( "%s\n" % interval ) 87 out_file.write( "%s\n" % interval )
86 except ParseError, exc: 88 except ParseError as exc:
87 out_file.close() 89 out_file.close()
88 fail( "Invalid file format: %s" % str( exc ) ) 90 fail( "Invalid file format: %s" % str( exc ) )
89 91
90 out_file.close() 92 out_file.close()
91 93
92 if g1.skipped > 0: 94 if g1.skipped > 0:
93 print skipped( g1, filedesc="" ) 95 print(skipped( g1, filedesc="" ))
96
94 97
95 if __name__ == "__main__": 98 if __name__ == "__main__":
96 main() 99 main()