/tools/fastq/fastq_paired_end_splitter.py
Python | 33 lines | 27 code | 4 blank | 2 comment | 7 complexity | 64c7e8b5d571e91565b8701af9e9e281 MD5 | raw file
1#Dan Blankenberg 2import sys, os, shutil 3from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqSplitter 4 5def 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 32if __name__ == "__main__": 33 main()