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1 #Dan Blankenberg
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2 from optparse import OptionParser
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3 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
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4
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5 def mean( score_list ):
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6 return float( sum( score_list ) ) / float( len( score_list ) )
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7
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8 ACTION_METHODS = { 'min':min, 'max':max, 'sum':sum, 'mean':mean }
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9
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10 def compare( aggregated_value, operator, threshold_value ):
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11 if operator == '>':
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12 return aggregated_value > threshold_value
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13 elif operator == '>=':
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14 return aggregated_value >= threshold_value
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15 elif operator == '==':
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16 return aggregated_value == threshold_value
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17 elif operator == '<':
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18 return aggregated_value < threshold_value
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19 elif operator == '<=':
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20 return aggregated_value <= threshold_value
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21 elif operator == '!=':
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22 return aggregated_value != threshold_value
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23
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24 def exclude( value_list, exclude_indexes ):
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25 rval = []
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26 for i, val in enumerate( value_list ):
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27 if i not in exclude_indexes:
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28 rval.append( val )
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29 return rval
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30
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31 def exclude_and_compare( aggregate_action, aggregate_list, operator, threshold_value, exclude_indexes = None ):
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32 if not aggregate_list or compare( aggregate_action( aggregate_list ), operator, threshold_value ):
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33 return True
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34 if exclude_indexes:
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35 for exclude_index in exclude_indexes:
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36 excluded_list = exclude( aggregate_list, exclude_index )
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37 if not excluded_list or compare( aggregate_action( excluded_list ), operator, threshold_value ):
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38 return True
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39 return False
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40
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41 def main():
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42 usage = "usage: %prog [options] input_file output_file"
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43 parser = OptionParser( usage=usage )
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44 parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'cssanger', 'solexa', 'illumina' ), help='FASTQ variant type' )
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45 parser.add_option( '-s', '--window_size', type="int", dest='window_size', default='1', help='Window size' )
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46 parser.add_option( '-t', '--window_step', type="int", dest='window_step', default='1', help='Window step' )
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47 parser.add_option( '-e', '--trim_ends', type="choice", dest='trim_ends', default='53', choices=('5','3','53','35' ), help='Ends to Trim' )
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48 parser.add_option( '-a', '--aggregation_action', type="choice", dest='aggregation_action', default='min', choices=('min','max','sum','mean' ), help='Aggregate action for window' )
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49 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' )
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50 parser.add_option( '-c', '--score_comparison', type="choice", dest='score_comparison', default='>=', choices=('>','>=','==','<', '<=', '!=' ), help='Keep read when aggregate score is' )
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51 parser.add_option( '-q', '--quality_score', type="float", dest='quality_score', default='0', help='Quality Score' )
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52 parser.add_option( "-k", "--keep_zero_length", action="store_true", dest="keep_zero_length", default=False, help="Keep reads with zero length")
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53 ( options, args ) = parser.parse_args()
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54
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55 if len ( args ) != 2:
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56 parser.error( "Need to specify an input file and an output file" )
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57
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58 if options.window_size < 1:
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59 parser.error( 'You must specify a strictly positive window size' )
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60
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61 if options.window_step < 1:
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62 parser.error( 'You must specify a strictly positive step size' )
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63
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64 #determine an exhaustive list of window indexes that can be excluded from aggregation
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65 exclude_window_indexes = []
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66 last_exclude_indexes = []
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67 for exclude_count in range( min( options.exclude_count, options.window_size ) ):
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68 if last_exclude_indexes:
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69 new_exclude_indexes = []
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70 for exclude_list in last_exclude_indexes:
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71 for window_index in range( options.window_size ):
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72 if window_index not in exclude_list:
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73 new_exclude = sorted( exclude_list + [ window_index ] )
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74 if new_exclude not in exclude_window_indexes + new_exclude_indexes:
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75 new_exclude_indexes.append( new_exclude )
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76 exclude_window_indexes += new_exclude_indexes
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77 last_exclude_indexes = new_exclude_indexes
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78 else:
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79 for window_index in range( options.window_size ):
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80 last_exclude_indexes.append( [ window_index ] )
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81 exclude_window_indexes = list( last_exclude_indexes )
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82
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83 out = fastqWriter( open( args[1], 'wb' ), format = options.format )
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84 action = ACTION_METHODS[ options.aggregation_action ]
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85
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86 num_reads = None
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87 num_reads_excluded = 0
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88 for num_reads, fastq_read in enumerate( fastqReader( open( args[0] ), format = options.format ) ):
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89 for trim_end in options.trim_ends:
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90 quality_list = fastq_read.get_decimal_quality_scores()
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91 if trim_end == '5':
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92 lwindow_position = 0 #left position of window
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93 while True:
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94 if lwindow_position >= len( quality_list ):
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95 fastq_read.sequence = ''
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96 fastq_read.quality = ''
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97 break
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98 if exclude_and_compare( action, quality_list[ lwindow_position:lwindow_position + options.window_size ], options.score_comparison, options.quality_score, exclude_window_indexes ):
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99 fastq_read = fastq_read.slice( lwindow_position, None )
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100 break
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101 lwindow_position += options.window_step
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102 else:
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103 rwindow_position = len( quality_list ) #right position of window
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104 while True:
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105 lwindow_position = rwindow_position - options.window_size #left position of window
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106 if rwindow_position <= 0 or lwindow_position < 0:
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107 fastq_read.sequence = ''
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108 fastq_read.quality = ''
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109 break
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110 if exclude_and_compare( action, quality_list[ lwindow_position:rwindow_position ], options.score_comparison, options.quality_score, exclude_window_indexes ):
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111 fastq_read = fastq_read.slice( None, rwindow_position )
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112 break
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113 rwindow_position -= options.window_step
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114 if options.keep_zero_length or len( fastq_read ):
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115 out.write( fastq_read )
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116 else:
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117 num_reads_excluded += 1
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118 out.close()
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119 if num_reads is None:
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120 print "No valid FASTQ reads could be processed."
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121 else:
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122 print "%i FASTQ reads were processed." % ( num_reads + 1 )
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123 if num_reads_excluded:
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124 print "%i reads of zero length were excluded from the output." % num_reads_excluded
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125
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126 if __name__ == "__main__": main()
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