root/galaxy-central/tools/fastq/fastq_paired_end_splitter.py @ 3

#Dan Blankenberg
import sys, os, shutil
from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqSplitter

def main():
    #Read command line arguments
    input_filename = sys.argv[1]
    input_type = sys.argv[2] or 'sanger'
    output1_filename = sys.argv[3]
    output2_filename = sys.argv[4]
    
    splitter = fastqSplitter()
    out1 = fastqWriter( open( output1_filename, 'wb' ), format = input_type )
    out2 = fastqWriter( open( output2_filename, 'wb' ), format = input_type )
    
    i = None
    skip_count = 0
    for i, fastq_read in enumerate( fastqReader( open( input_filename, 'rb' ), format = input_type ) ):
        read1, read2 = splitter.split( fastq_read )
        if read1 and read2:
            out1.write( read1 )
            out2.write( read2 )
        else:
            skip_count += 1
    out1.close()
    out2.close()
    if i is None:
        print "Your file contains no valid FASTQ reads."
    else:
        print 'Split %s of %s reads (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )

if __name__ == "__main__":
    main()