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