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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, fastqNamedReader, fastqWriter, fastqJoiner
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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 input1_filename = sys.argv[1]
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8 input1_type = sys.argv[2] or 'sanger'
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9 input2_filename = sys.argv[3]
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10 input2_type = sys.argv[4] or 'sanger'
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11 output_filename = sys.argv[5]
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12
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13 if input1_type != input2_type:
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14 print "WARNING: You are trying to join files of two different types: %s and %s." % ( input1_type, input2_type )
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15
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16 input2 = fastqNamedReader( open( input2_filename, 'rb' ), input2_type )
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17 joiner = fastqJoiner( input1_type )
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18 out = fastqWriter( open( output_filename, 'wb' ), format = input1_type )
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19
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20 i = None
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21 skip_count = 0
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22 for i, fastq_read in enumerate( fastqReader( open( input1_filename, 'rb' ), format = input1_type ) ):
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23 identifier = joiner.get_paired_identifier( fastq_read )
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24 fastq_paired = input2.get( identifier )
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25 if fastq_paired is None:
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26 skip_count += 1
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27 else:
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28 out.write( joiner.join( fastq_read, fastq_paired ) )
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29 out.close()
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30
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31 if i is None:
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32 print "Your file contains no valid FASTQ reads."
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33 else:
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34 print input2.has_data()
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35 print 'Joined %s of %s read pairs (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
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36
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37 if __name__ == "__main__":
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38 main()
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