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101 lines
2.8 KiB
Python
101 lines
2.8 KiB
Python
#!/usr/bin/env python
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import sys
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import optparse
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import re
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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def main():
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usage = """%prog [options]
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options (listed below) default to 'None' if omitted
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"""
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parser = optparse.OptionParser(usage=usage)
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parser.add_option(
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'-f','--input_sam_file',
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metavar="INPUT_SAM_FILE",
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dest='input_sam',
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default = False,
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help='Name of the SAM file to be filtered. STDIN is default')
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parser.add_option(
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'-c','--flag_column',
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dest='flag_col',
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default = '2',
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help='Column containing SAM bitwise flag. 1-based')
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parser.add_option(
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'-s','--start_column',
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dest='start_col',
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default = '4',
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help='Column containing position. 1-based')
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parser.add_option(
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'-g','--cigar_column',
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dest='cigar_col',
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default = '6',
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help='Column containing CIGAR or extended CIGAR string')
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parser.add_option(
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'-r','--ref_column',
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dest='ref_col',
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default = '3',
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help='Column containing name of the refernce sequence coordinate. 1-based')
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parser.add_option(
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'-e','--read_column',
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dest='read_col',
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default = '1',
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help='Column containing read name. 1-based')
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parser.add_option(
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'-d','--debug',
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dest='debug',
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action='store_true',
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default = False,
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help='Print debugging info')
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parser.add_option(
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'-p','--print_all',
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dest='prt_all',
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action='store_true',
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default = False,
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help='Print coordinates and original SAM?')
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options, args = parser.parse_args()
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if options.input_sam:
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infile = open ( options.input_sam, 'r')
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else:
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infile = sys.stdin
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cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' )
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for line in infile:
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line = line.rstrip( '\r\n' )
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if line and not line.startswith( '#' ) and not line.startswith( '@' ) :
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fields = line.split( '\t' )
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start = int( fields[ int( options.start_col ) - 1 ] ) - 1
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end = 0
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for op in cigar.findall( fields[ int( options.cigar_col) - 1 ] ):
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end += int( op[ 0:len( op ) - 1 ] )
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strand = '+'
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if bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0010 ):
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strand = '-'
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read_name = fields[ int( options.read_col ) - 1 ]
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ref_name = fields[ int( options.ref_col ) - 1 ]
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if options.prt_all:
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print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line)
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else:
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print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand)
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if __name__ == "__main__": main()
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