/tools/new_operations/gops_merge.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 71 lines · 53 code · 9 blank · 9 comment · 15 complexity · 97476837c90f5d77e4482cc929a54d45 MD5 · raw file
- #!/usr/bin/env python
- """
- Merge overlaping regions.
- usage: %prog in_file out_file
- -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
- -m, --mincols=N: Require this much overlap (default 1bp)
- -3, --threecol: Output 3 column bed
- """
- from galaxy import eggs
- import pkg_resources
- pkg_resources.require( "bx-python" )
- import sys, traceback, fileinput
- from warnings import warn
- from bx.intervals import *
- from bx.intervals.io import *
- from bx.intervals.operations.merge import *
- from bx.cookbook import doc_optparse
- from galaxy.tools.util.galaxyops import *
- assert sys.version_info[:2] >= ( 2, 4 )
- def main():
- mincols = 1
- upstream_pad = 0
- downstream_pad = 0
- options, args = doc_optparse.parse( __doc__ )
- try:
- chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
- if options.mincols: mincols = int( options.mincols )
- in_fname, out_fname = args
- except:
- doc_optparse.exception()
- g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
- chrom_col=chr_col_1,
- start_col=start_col_1,
- end_col=end_col_1,
- strand_col = strand_col_1,
- fix_strand=True )
- out_file = open( out_fname, "w" )
- try:
- for line in merge(g1,mincols=mincols):
- if options.threecol:
- if type( line ) is GenomicInterval:
- out_file.write( "%s\t%s\t%s\n" % ( line.chrom, str( line.startCol ), str( line.endCol ) ) )
- elif type( line ) is list:
- out_file.write( "%s\t%s\t%s\n" % ( line[chr_col_1], str( line[start_col_1] ), str( line[end_col_1] ) ) )
- else:
- out_file.write( "%s\n" % line )
- else:
- if type( line ) is GenomicInterval:
- out_file.write( "%s\n" % "\t".join( line.fields ) )
- elif type( line ) is list:
- out_file.write( "%s\n" % "\t".join( line ) )
- else:
- out_file.write( "%s\n" % line )
- except ParseError, exc:
- out_file.close()
- fail( "Invalid file format: %s" % str( exc ) )
- out_file.close()
- if g1.skipped > 0:
- print skipped( g1, filedesc=" of 1st dataset" )
- if __name__ == "__main__":
- main()