Mercurial > repos > devteam > fastq_paired_end_splitter
view fastq_paired_end_splitter.py @ 0:5943afe0f24d draft
Imported from capsule None
author | devteam |
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date | Thu, 23 Jan 2014 12:32:16 -0500 |
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#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()