#Dan Blankenberg from optparse import OptionParser from galaxy_utils.sequence.fastq import fastqReader, fastqWriter def mean( score_list ): return float( sum( score_list ) ) / float( len( score_list ) ) ACTION_METHODS = { 'min':min, 'max':max, 'sum':sum, 'mean':mean } def compare( aggregated_value, operator, threshold_value ): if operator == '>': return aggregated_value > threshold_value elif operator == '>=': return aggregated_value >= threshold_value elif operator == '==': return aggregated_value == threshold_value elif operator == '<': return aggregated_value < threshold_value elif operator == '<=': return aggregated_value <= threshold_value elif operator == '!=': return aggregated_value != threshold_value def exclude( value_list, exclude_indexes ): rval = [] for i, val in enumerate( value_list ): if i not in exclude_indexes: rval.append( val ) return rval def exclude_and_compare( aggregate_action, aggregate_list, operator, threshold_value, exclude_indexes = None ): if not aggregate_list or compare( aggregate_action( aggregate_list ), operator, threshold_value ): return True if exclude_indexes: for exclude_index in exclude_indexes: excluded_list = exclude( aggregate_list, exclude_index ) if not excluded_list or compare( aggregate_action( excluded_list ), operator, threshold_value ): return True return False def main(): usage = "usage: %prog [options] input_file output_file" parser = OptionParser( usage=usage ) parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'cssanger', 'solexa', 'illumina' ), help='FASTQ variant type' ) parser.add_option( '-s', '--window_size', type="int", dest='window_size', default='1', help='Window size' ) parser.add_option( '-t', '--window_step', type="int", dest='window_step', default='1', help='Window step' ) parser.add_option( '-e', '--trim_ends', type="choice", dest='trim_ends', default='53', choices=('5','3','53','35' ), help='Ends to Trim' ) parser.add_option( '-a', '--aggregation_action', type="choice", dest='aggregation_action', default='min', choices=('min','max','sum','mean' ), help='Aggregate action for window' ) parser.add_option( '-x', '--exclude_count', type="int", dest='exclude_count', default='0', help='Maximum number of bases to exclude from the window during aggregation' ) parser.add_option( '-c', '--score_comparison', type="choice", dest='score_comparison', default='>=', choices=('>','>=','==','<', '<=', '!=' ), help='Keep read when aggregate score is' ) parser.add_option( '-q', '--quality_score', type="float", dest='quality_score', default='0', help='Quality Score' ) parser.add_option( "-k", "--keep_zero_length", action="store_true", dest="keep_zero_length", default=False, help="Keep reads with zero length") ( options, args ) = parser.parse_args() if len ( args ) != 2: parser.error( "Need to specify an input file and an output file" ) if options.window_size < 1: parser.error( 'You must specify a strictly positive window size' ) if options.window_step < 1: parser.error( 'You must specify a strictly positive step size' ) #determine an exhaustive list of window indexes that can be excluded from aggregation exclude_window_indexes = [] last_exclude_indexes = [] for exclude_count in range( min( options.exclude_count, options.window_size ) ): if last_exclude_indexes: new_exclude_indexes = [] for exclude_list in last_exclude_indexes: for window_index in range( options.window_size ): if window_index not in exclude_list: new_exclude = sorted( exclude_list + [ window_index ] ) if new_exclude not in exclude_window_indexes + new_exclude_indexes: new_exclude_indexes.append( new_exclude ) exclude_window_indexes += new_exclude_indexes last_exclude_indexes = new_exclude_indexes else: for window_index in range( options.window_size ): last_exclude_indexes.append( [ window_index ] ) exclude_window_indexes = list( last_exclude_indexes ) out = fastqWriter( open( args[1], 'wb' ), format = options.format ) action = ACTION_METHODS[ options.aggregation_action ] num_reads = None num_reads_excluded = 0 for num_reads, fastq_read in enumerate( fastqReader( open( args[0] ), format = options.format ) ): for trim_end in options.trim_ends: quality_list = fastq_read.get_decimal_quality_scores() if trim_end == '5': lwindow_position = 0 #left position of window while True: if lwindow_position >= len( quality_list ): fastq_read.sequence = '' fastq_read.quality = '' break if exclude_and_compare( action, quality_list[ lwindow_position:lwindow_position + options.window_size ], options.score_comparison, options.quality_score, exclude_window_indexes ): fastq_read = fastq_read.slice( lwindow_position, None ) break lwindow_position += options.window_step else: rwindow_position = len( quality_list ) #right position of window while True: lwindow_position = rwindow_position - options.window_size #left position of window if rwindow_position <= 0 or lwindow_position < 0: fastq_read.sequence = '' fastq_read.quality = '' break if exclude_and_compare( action, quality_list[ lwindow_position:rwindow_position ], options.score_comparison, options.quality_score, exclude_window_indexes ): fastq_read = fastq_read.slice( None, rwindow_position ) break rwindow_position -= options.window_step if options.keep_zero_length or len( fastq_read ): out.write( fastq_read ) else: num_reads_excluded += 1 out.close() if num_reads is None: print "No valid FASTQ reads could be processed." else: print "%i FASTQ reads were processed." % ( num_reads + 1 ) if num_reads_excluded: print "%i reads of zero length were excluded from the output." % num_reads_excluded if __name__ == "__main__": main()