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1 #Dan Blankenberg
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2 import sys
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3 from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
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4
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5 def main():
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6 input_filename = sys.argv[1]
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7 input_type = sys.argv[2]
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8 output_filename = sys.argv[3]
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9 output_type = sys.argv[4]
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10 force_quality_encoding = sys.argv[5]
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11 summarize_input = sys.argv[6] == 'summarize_input'
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12 if force_quality_encoding == 'None':
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13 force_quality_encoding = None
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14
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15 aggregator = fastqAggregator()
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16 out = fastqWriter( open( output_filename, 'wb' ), format = output_type, force_quality_encoding = force_quality_encoding )
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17 read_count = None
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18 if summarize_input:
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19 reader = fastqVerboseErrorReader
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20 else:
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21 reader = fastqReader
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22 for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type, apply_galaxy_conventions = True ) ):
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23 if summarize_input:
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24 aggregator.consume_read( fastq_read )
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25 out.write( fastq_read )
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26 out.close()
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27
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28 if read_count is not None:
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29 print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type )
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30 if input_type != output_type and 'solexa' in [ input_type, output_type ]:
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31 print "Converted between Solexa and PHRED scores."
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32 if summarize_input:
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33 print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" )
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34 ascii_range = aggregator.get_ascii_range()
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35 decimal_range = aggregator.get_decimal_range()
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36 print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed
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37 print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] )
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38 else:
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39 print "No valid FASTQ reads were provided."
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40
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41
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42 if __name__ == "__main__": main()
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