Mercurial > repos > devteam > fastq_masker_by_quality

comparison fastq_masker_by_quality.py @ 0:5a7b5751617b draft

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:25:39 -0500
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-1:000000000000 0:5a7b5751617b
1 #Dan Blankenberg
2 import string
3 from optparse import OptionParser
4 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
5
6
7 def get_score_comparer( operator ):
8 if operator == 'gt':
9 return compare_gt
10 elif operator == 'ge':
11 return compare_ge
12 elif operator == 'eq':
13 return compare_eq
14 elif operator == 'lt':
15 return compare_lt
16 elif operator == 'le':
17 return compare_le
18 elif operator == 'ne':
19 return compare_ne
20 raise 'Invalid operator provided: %s' % operator
21
22 def compare_gt( quality_score, threshold_value ):
23 return quality_score > threshold_value
24
25 def compare_ge( quality_score, threshold_value ):
26 return quality_score >= threshold_value
27
28 def compare_eq( quality_score, threshold_value ):
29 return quality_score == threshold_value
30
31 def compare_ne( quality_score, threshold_value ):
32 return quality_score != threshold_value
33
34 def compare_lt( quality_score, threshold_value ):
35 return quality_score < threshold_value
36
37 def compare_le( quality_score, threshold_value ):
38 return quality_score <= threshold_value
39
40 class BaseReplacer( object ):
41 def __init__( self, replace_character ):
42 self.replace_character = replace_character
43 def __call__( self, base_character ):
44 return self.replace_character
45
46 def main():
47 usage = "usage: %prog [options] input_file output_file"
48 parser = OptionParser( usage=usage )
49 parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'solexa', 'illumina' ), help='FASTQ variant type' )
50 parser.add_option( '-m', '--mask_character', dest='mask_character', default='N', help='Mask Character to use' )
51 parser.add_option( '-c', '--score_comparison', type="choice", dest='score_comparison', default='le', choices=('gt','ge','eq','lt', 'le', 'ne' ), help='Mask base when score is' )
52 parser.add_option( '-s', '--quality_score', type="float", dest='quality_score', default='0', help='Quality Score' )
53 parser.add_option( "-l", "--lowercase", action="store_true", dest="lowercase", default=False, help="Use lowercase masking")
54 ( options, args ) = parser.parse_args()
55
56 if len ( args ) != 2:
57 parser.error( "Need to specify an input file and an output file" )
58
59 score_comparer = get_score_comparer( options.score_comparison )
60
61 if options.lowercase:
62 base_masker = string.lower
63 else:
64 base_masker = BaseReplacer( options.mask_character )
65
66 out = fastqWriter( open( args[1], 'wb' ), format = options.format )
67
68 num_reads = None
69 num_reads_excluded = 0
70 for num_reads, fastq_read in enumerate( fastqReader( open( args[0] ), format = options.format ) ):
71 sequence_list = list( fastq_read.sequence )
72 for i, quality_score in enumerate( fastq_read.get_decimal_quality_scores() ):
73 if score_comparer( quality_score, options.quality_score ):
74 sequence_list[ i ] = base_masker( sequence_list[ i ] )
75 fastq_read.sequence = "".join( sequence_list )
76 out.write( fastq_read )
77
78 if num_reads is not None:
79 print "Processed %i %s reads." % ( num_reads + 1, options.format )
80 else:
81 print "No valid FASTQ reads were provided."
82
83 if __name__ == "__main__": main()