picard_interval_list_to_bed6_converter.py

#!/usr/bin/env python
#Dan Blankenberg

import sys

assert sys.version_info[:2] >= ( 2, 5 )
HEADER_STARTS_WITH = ( '@' )

def __main__():
    input_name = sys.argv[1]
    output_name = sys.argv[2]
    skipped_lines = 0
    first_skipped_line = 0
    header_lines = 0
    out = open( output_name, 'w' )
    i = 0
    for i, line in enumerate( open( input_name ) ):
	complete_interval = False
	line = line.rstrip( '\r\n' )
	if line:
	    if line.startswith( HEADER_STARTS_WITH ):
		header_lines += 1
	    else:
		try:
		    elems = line.split( '\t' )
		    if len( elems ) >= 5:
			complete_interval = True
		    out.write( '%s\t%s\t%s\t%s\t0\t%s\n' % ( elems[0], int(elems[1])-1, elems[2], elems[4], elems[3] ) )
		except Exception, e:
		    print e
		    skipped_lines += 1
		    if not first_skipped_line:
			first_skipped_line = i + 1
	else:
	    skipped_lines += 1
	    if not first_skipped_line:
		first_skipped_line = i + 1
    out.close()
    info_msg = "%i lines converted to BED.  " % ( i + 1 - skipped_lines )
    if skipped_lines > 0:
	info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
    print info_msg

if __name__ == "__main__": __main__()