# HG changeset patch # User devteam # Date 1506797914 14400 # Node ID eb592e9ec47a6acad874cc4a492096b136461498 # Parent 9d234265981e5f18c0eba06af4f93a2abfed5471 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a diff -r 9d234265981e -r eb592e9ec47a fastq_masker_by_quality.py --- a/fastq_masker_by_quality.py Wed Nov 11 12:41:24 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -#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() diff -r 9d234265981e -r eb592e9ec47a fastq_masker_by_quality.xml --- a/fastq_masker_by_quality.xml Wed Nov 11 12:41:24 2015 -0500 +++ b/fastq_masker_by_quality.xml Sat Sep 30 14:58:34 2017 -0400 @@ -1,61 +1,59 @@ - - by quality score - - galaxy_sequence_utils - - fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}' - #if $mask_type.value == 'lowercase' - --lowercase - #else - -m '${mask_type}' - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + by quality score + + galaxy_sequence_utils + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - 10.1093/bioinformatics/btq281 - - + ]]> + + 10.1093/bioinformatics/btq281 + diff -r 9d234265981e -r eb592e9ec47a tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:41:24 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -