Subsample.txt: Difference between revisions

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>Noi
(Created page with "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...")
 
>Noi
mNo edit summary
Line 1: Line 1:
import sys, random
import sys, random
import HTSeq
import HTSeq
 
fraction = float( sys.argv[1] )
fraction = float( sys.argv[1] )
in1 = iter( HTSeq.FastqReader( sys.argv[2] ) )
in1 = iter( HTSeq.FastqReader( sys.argv[2] ) )
in2 = iter( HTSeq.FastqReader( sys.argv[3] ) )
in2 = iter( HTSeq.FastqReader( sys.argv[3] ) )
out1 = open( sys.argv[4], "w" )
out1 = open( sys.argv[4], "w" )
out2 = open( sys.argv[5], "w" )
out2 = open( sys.argv[5], "w" )
 
while True:
while True:
   read1 = next( in1 )
   read1 = next( in1 )
   read2 = next( in2 )
   read2 = next( in2 )
Line 14: Line 14:
       read1.write_to_fastq_file( out1 )
       read1.write_to_fastq_file( out1 )
       read2.write_to_fastq_file( out2 )
       read2.write_to_fastq_file( out2 )
     
       
out1.close()
out1.close()
out2.close()
out2.close()

Revision as of 22:40, 20 July 2014

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()