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1 #Dan Blankenberg
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2 import sys, os, shutil
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3 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqSplitter
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4
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5 def main():
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6 #Read command line arguments
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7 input_filename = sys.argv[1]
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8 input_type = sys.argv[2] or 'sanger'
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9 output1_filename = sys.argv[3]
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10 output2_filename = sys.argv[4]
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11
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12 splitter = fastqSplitter()
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13 out1 = fastqWriter( open( output1_filename, 'wb' ), format = input_type )
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14 out2 = fastqWriter( open( output2_filename, 'wb' ), format = input_type )
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15
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16 i = None
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17 skip_count = 0
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18 for i, fastq_read in enumerate( fastqReader( open( input_filename, 'rb' ), format = input_type ) ):
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19 read1, read2 = splitter.split( fastq_read )
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20 if read1 and read2:
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21 out1.write( read1 )
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22 out2.write( read2 )
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23 else:
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24 skip_count += 1
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25 out1.close()
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26 out2.close()
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27 if i is None:
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28 print "Your file contains no valid FASTQ reads."
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29 else:
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30 print 'Split %s of %s reads (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
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31
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32 if __name__ == "__main__":
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33 main()
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