# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li kanwei@gmail.com # Date 1289677046 18000 # Node ID 98009db17cb2b21db626fc9c185a8fd22109a4cd # Parent cadf13f67c6593d99f8134ba10baa211a026439b Refactor sam_bitwise_flag_filter tool, simplifying it and making it faster, especially when there are multiple flag criteria

--- a/tools/samtools/sam_bitwise_flag_filter.py +++ b/tools/samtools/sam_bitwise_flag_filter.py @@ -1,4 +1,5 @@ #!/usr/bin/env python +# Refactored on 11/13/2010 by Kanwei Li

import sys import optparse @@ -104,74 +105,45 @@ options (listed below) default to 'None' default = '2', help='Column containing SAM bitwise flag. 1-based')

- parser.add_option( - '-d','--debug', - dest='debug', - action='store_true', - default = False, - help='Print debugging info') - options, args = parser.parse_args()

if options.input_sam: infile = open ( options.input_sam, 'r') else: infile = sys.stdin - - option_values = { '0': False, '1': True, None: None } - - states = []; - states.append( option_values[ options.is_paired ] ) - states.append( option_values[ options.is_proper_pair ] ) - states.append( option_values[ options.is_unmapped ] ) - states.append( option_values[ options.mate_is_unmapped ] ) - states.append( option_values[ options.query_strand ] ) - states.append( option_values[ options.mate_strand ] ) - states.append( option_values[ options.is_first ] ) - states.append( option_values[ options.is_second ] ) - states.append( option_values[ options.is_not_primary ] ) - states.append( option_values[ options.is_bad_quality ] ) - states.append( option_values[ options.is_duplicate ] ) - + + opt_ary = [ + options.is_paired, + options.is_proper_pair, + options.is_unmapped, + options.mate_is_unmapped, + options.query_strand, + options.mate_strand, + options.is_first, + options.is_second, + options.is_not_primary, + options.is_bad_quality, + options.is_duplicate + ] + + opt_map = { '0': False, '1': True } + used_indices = [(index, opt_map[opt]) for index, opt in enumerate(opt_ary) if opt is not None] + flag_col = int( options.flag_col ) - 1 + for line in infile: line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ) and not line.startswith( '@' ) : fields = line.split( '\t' ) - sam_states = [] - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0001 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0002 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0004 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0008 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0010 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0020 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0040 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0080 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0100 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0200 ) ) - sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0400 ) ) - - joined_states = zip(states,sam_states) - searchable_fields = [] - - for i in range( len( joined_states ) ): - if joined_states[i][0] != None: - searchable_fields.append( joined_states[ i ] ) + flags = int( fields[flag_col] )

valid_line = True - - for i in range( len( searchable_fields ) ): - if searchable_fields[i][0] != searchable_fields[i][1]: + for index, opt_bool in used_indices: + if bool(flags & 0x0001 << index) != opt_bool: valid_line = False + break

if valid_line: print line - if options.debug: - for i in range( len( joined_states ) ): - print i, joined_states[i][0], joined_states[i][1] - -# if skipped_lines > 0: -# print 'Skipped %d invalid lines' % skipped_lines -

if __name__ == "__main__": main()