/tools/fastq/fastq_masker_by_quality.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 83 lines · 65 code · 17 blank · 1 comment · 15 complexity · 03c266b3b797243d51efbe9f3ba79a72 MD5 · raw file
- #Dan Blankenberg
- import string
- from optparse import OptionParser
- from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
- def get_score_comparer( operator ):
- if operator == 'gt':
- return compare_gt
- elif operator == 'ge':
- return compare_ge
- elif operator == 'eq':
- return compare_eq
- elif operator == 'lt':
- return compare_lt
- elif operator == 'le':
- return compare_le
- elif operator == 'ne':
- return compare_ne
- raise 'Invalid operator provided: %s' % operator
- def compare_gt( quality_score, threshold_value ):
- return quality_score > threshold_value
- def compare_ge( quality_score, threshold_value ):
- return quality_score >= threshold_value
- def compare_eq( quality_score, threshold_value ):
- return quality_score == threshold_value
- def compare_ne( quality_score, threshold_value ):
- return quality_score != threshold_value
- def compare_lt( quality_score, threshold_value ):
- return quality_score < threshold_value
- def compare_le( quality_score, threshold_value ):
- return quality_score <= threshold_value
- class BaseReplacer( object ):
- def __init__( self, replace_character ):
- self.replace_character = replace_character
- def __call__( self, base_character ):
- return self.replace_character
- 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', 'solexa', 'illumina' ), help='FASTQ variant type' )
- parser.add_option( '-m', '--mask_character', dest='mask_character', default='N', help='Mask Character to use' )
- 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' )
- parser.add_option( '-s', '--quality_score', type="float", dest='quality_score', default='0', help='Quality Score' )
- parser.add_option( "-l", "--lowercase", action="store_true", dest="lowercase", default=False, help="Use lowercase masking")
- ( options, args ) = parser.parse_args()
-
- if len ( args ) != 2:
- parser.error( "Need to specify an input file and an output file" )
-
- score_comparer = get_score_comparer( options.score_comparison )
-
- if options.lowercase:
- base_masker = string.lower
- else:
- base_masker = BaseReplacer( options.mask_character )
-
- out = fastqWriter( open( args[1], 'wb' ), format = options.format )
-
- num_reads = None
- num_reads_excluded = 0
- for num_reads, fastq_read in enumerate( fastqReader( open( args[0] ), format = options.format ) ):
- sequence_list = list( fastq_read.sequence )
- for i, quality_score in enumerate( fastq_read.get_decimal_quality_scores() ):
- if score_comparer( quality_score, options.quality_score ):
- sequence_list[ i ] = base_masker( sequence_list[ i ] )
- fastq_read.sequence = "".join( sequence_list )
- out.write( fastq_read )
-
- if num_reads is not None:
- print "Processed %i %s reads." % ( num_reads + 1, options.format )
- else:
- print "No valid FASTQ reads were provided."
- if __name__ == "__main__": main()