--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq/fastq_masker_by_quality.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,83 @@
+#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()