Subsample.txt

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import sys, random
import HTSeq

fraction = float( sys.argv[1] )
in1 = iter( HTSeq.FastqReader( sys.argv[2] ) )
in2 = iter( HTSeq.FastqReader( sys.argv[3] ) )
out1 = open( sys.argv[4], "w" )
out2 = open( sys.argv[5], "w" )

while True:
  read1 = next( in1 )
  read2 = next( in2 )
  if random.random() < fraction:
     read1.write_to_fastq_file( out1 )
     read2.write_to_fastq_file( out2 )
       
out1.close()
out2.close()