Mercurial > repos > xuebing > sharplabtool

comparison tools/fastq/fastq_trimmer_by_quality.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #Dan Blankenberg
2 from optparse import OptionParser
3 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
4
5 def mean( score_list ):
6 return float( sum( score_list ) ) / float( len( score_list ) )
7
8 ACTION_METHODS = { 'min':min, 'max':max, 'sum':sum, 'mean':mean }
9
10 def compare( aggregated_value, operator, threshold_value ):
11 if operator == '>':
12 return aggregated_value > threshold_value
13 elif operator == '>=':
14 return aggregated_value >= threshold_value
15 elif operator == '==':
16 return aggregated_value == threshold_value
17 elif operator == '<':
18 return aggregated_value < threshold_value
19 elif operator == '<=':
20 return aggregated_value <= threshold_value
21 elif operator == '!=':
22 return aggregated_value != threshold_value
23
24 def exclude( value_list, exclude_indexes ):
25 rval = []
26 for i, val in enumerate( value_list ):
27 if i not in exclude_indexes:
28 rval.append( val )
29 return rval
30
31 def exclude_and_compare( aggregate_action, aggregate_list, operator, threshold_value, exclude_indexes = None ):
32 if not aggregate_list or compare( aggregate_action( aggregate_list ), operator, threshold_value ):
33 return True
34 if exclude_indexes:
35 for exclude_index in exclude_indexes:
36 excluded_list = exclude( aggregate_list, exclude_index )
37 if not excluded_list or compare( aggregate_action( excluded_list ), operator, threshold_value ):
38 return True
39 return False
40
41 def main():
42 usage = "usage: %prog [options] input_file output_file"
43 parser = OptionParser( usage=usage )
44 parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'cssanger', 'solexa', 'illumina' ), help='FASTQ variant type' )
45 parser.add_option( '-s', '--window_size', type="int", dest='window_size', default='1', help='Window size' )
46 parser.add_option( '-t', '--window_step', type="int", dest='window_step', default='1', help='Window step' )
47 parser.add_option( '-e', '--trim_ends', type="choice", dest='trim_ends', default='53', choices=('5','3','53','35' ), help='Ends to Trim' )
48 parser.add_option( '-a', '--aggregation_action', type="choice", dest='aggregation_action', default='min', choices=('min','max','sum','mean' ), help='Aggregate action for window' )
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' )
50 parser.add_option( '-c', '--score_comparison', type="choice", dest='score_comparison', default='>=', choices=('>','>=','==','<', '<=', '!=' ), help='Keep read when aggregate score is' )
51 parser.add_option( '-q', '--quality_score', type="float", dest='quality_score', default='0', help='Quality Score' )
52 parser.add_option( "-k", "--keep_zero_length", action="store_true", dest="keep_zero_length", default=False, help="Keep reads with zero length")
53 ( options, args ) = parser.parse_args()
54
55 if len ( args ) != 2:
56 parser.error( "Need to specify an input file and an output file" )
57
58 if options.window_size < 1:
59 parser.error( 'You must specify a strictly positive window size' )
60
61 if options.window_step < 1:
62 parser.error( 'You must specify a strictly positive step size' )
63
64 #determine an exhaustive list of window indexes that can be excluded from aggregation
65 exclude_window_indexes = []
66 last_exclude_indexes = []
67 for exclude_count in range( min( options.exclude_count, options.window_size ) ):
68 if last_exclude_indexes:
69 new_exclude_indexes = []
70 for exclude_list in last_exclude_indexes:
71 for window_index in range( options.window_size ):
72 if window_index not in exclude_list:
73 new_exclude = sorted( exclude_list + [ window_index ] )
74 if new_exclude not in exclude_window_indexes + new_exclude_indexes:
75 new_exclude_indexes.append( new_exclude )
76 exclude_window_indexes += new_exclude_indexes
77 last_exclude_indexes = new_exclude_indexes
78 else:
79 for window_index in range( options.window_size ):
80 last_exclude_indexes.append( [ window_index ] )
81 exclude_window_indexes = list( last_exclude_indexes )
82
83 out = fastqWriter( open( args[1], 'wb' ), format = options.format )
84 action = ACTION_METHODS[ options.aggregation_action ]
85
86 num_reads = None
87 num_reads_excluded = 0
88 for num_reads, fastq_read in enumerate( fastqReader( open( args[0] ), format = options.format ) ):
89 for trim_end in options.trim_ends:
90 quality_list = fastq_read.get_decimal_quality_scores()
91 if trim_end == '5':
92 lwindow_position = 0 #left position of window
93 while True:
94 if lwindow_position >= len( quality_list ):
95 fastq_read.sequence = ''
96 fastq_read.quality = ''
97 break
98 if exclude_and_compare( action, quality_list[ lwindow_position:lwindow_position + options.window_size ], options.score_comparison, options.quality_score, exclude_window_indexes ):
99 fastq_read = fastq_read.slice( lwindow_position, None )
100 break
101 lwindow_position += options.window_step
102 else:
103 rwindow_position = len( quality_list ) #right position of window
104 while True:
105 lwindow_position = rwindow_position - options.window_size #left position of window
106 if rwindow_position <= 0 or lwindow_position < 0:
107 fastq_read.sequence = ''
108 fastq_read.quality = ''
109 break
110 if exclude_and_compare( action, quality_list[ lwindow_position:rwindow_position ], options.score_comparison, options.quality_score, exclude_window_indexes ):
111 fastq_read = fastq_read.slice( None, rwindow_position )
112 break
113 rwindow_position -= options.window_step
114 if options.keep_zero_length or len( fastq_read ):
115 out.write( fastq_read )
116 else:
117 num_reads_excluded += 1
118 out.close()
119 if num_reads is None:
120 print "No valid FASTQ reads could be processed."
121 else:
122 print "%i FASTQ reads were processed." % ( num_reads + 1 )
123 if num_reads_excluded:
124 print "%i reads of zero length were excluded from the output." % num_reads_excluded
125
126 if __name__ == "__main__": main()