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comparison tools/fastq/fastq_paired_end_splitter.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #Dan Blankenberg
2 import sys, os, shutil
3 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqSplitter
4
5 def main():
6 #Read command line arguments
7 input_filename = sys.argv[1]
8 input_type = sys.argv[2] or 'sanger'
9 output1_filename = sys.argv[3]
10 output2_filename = sys.argv[4]
11
12 splitter = fastqSplitter()
13 out1 = fastqWriter( open( output1_filename, 'wb' ), format = input_type )
14 out2 = fastqWriter( open( output2_filename, 'wb' ), format = input_type )
15
16 i = None
17 skip_count = 0
18 for i, fastq_read in enumerate( fastqReader( open( input_filename, 'rb' ), format = input_type ) ):
19 read1, read2 = splitter.split( fastq_read )
20 if read1 and read2:
21 out1.write( read1 )
22 out2.write( read2 )
23 else:
24 skip_count += 1
25 out1.close()
26 out2.close()
27 if i is None:
28 print "Your file contains no valid FASTQ reads."
29 else:
30 print 'Split %s of %s reads (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
31
32 if __name__ == "__main__":
33 main()