[2] | 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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