Mercurial > repos > devteam > merge

comparison gops_merge.py @ 5:dfbbc0291b36 draft default tip

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/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:51:08 -0400
parents b9c97d3233bb
children
comparison
equal deleted inserted replaced
4:a2f62c0c0537 5:dfbbc0291b36
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 """ 2 """
3 Merge overlaping regions. 3 Merge overlapping regions.
4 4
5 usage: %prog in_file out_file 5 usage: %prog in_file out_file
6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file 6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
7 -m, --mincols=N: Require this much overlap (default 1bp) 7 -m, --mincols=N: Require this much overlap (default 1bp)
8 -3, --threecol: Output 3 column bed 8 -3, --threecol: Output 3 column bed
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.merge import merge 17 from bx.intervals.operations.merge import merge
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
53 out_file.write( "%s\n" % "\t".join( line.fields ) ) 56 out_file.write( "%s\n" % "\t".join( line.fields ) )
54 elif type( line ) is list: 57 elif type( line ) is list:
55 out_file.write( "%s\n" % "\t".join( line ) ) 58 out_file.write( "%s\n" % "\t".join( line ) )
56 else: 59 else:
57 out_file.write( "%s\n" % line ) 60 out_file.write( "%s\n" % line )
58 except ParseError, exc: 61 except ParseError as exc:
59 out_file.close() 62 out_file.close()
60 fail( "Invalid file format: %s" % str( exc ) ) 63 fail( "Invalid file format: %s" % str( exc ) )
61 64
62 out_file.close() 65 out_file.close()
63 66
64 if g1.skipped > 0: 67 if g1.skipped > 0:
65 print skipped( g1, filedesc=" of 1st dataset" ) 68 print(skipped( g1, filedesc=" of 1st dataset" ))
69
66 70
67 if __name__ == "__main__": 71 if __name__ == "__main__":
68 main() 72 main()