Python: Interleave Paired-End Reads

Here’s a simple script for interleaving paired-end fastq files. You’ll need to do this if you want to create input files for velvet. It requires python 2.7.

#!/usr/bin/env python # encoding: utf-8 import sys import argparse def interface(): parser = argparse.ArgumentParser() parser.add_argument('--rm-short-reads', type=int, help='Minimum number of base pairs \ either R1 or R2 read must be.') # add additional trimming/filtering functionality as needed. parser.add_argument('LEFT_INPUT', type=argparse.FileType('r'), default=sys.stdin, nargs='?', help='R1 reads.') parser.add_argument('RIGHT_INPUT', type=argparse.FileType('r'), default=sys.stdin, nargs='?', help='R2 reads.') parser.add_argument('INTERLEAVED_OUTPUT', type=argparse.FileType('w'), default=sys.stdout, nargs='?', help='Alignment file.') args = parser.parse_args() return args def process_reads(args): left = args.LEFT_INPUT right = args.RIGHT_INPUT fout = args.INTERLEAVED_OUTPUT # USING A WHILE LOOP MAKES THIS SUPER FAST # Details here: # http://effbot.org/zone/readline-performance.htm while 1: # process the first file left_id = left.readline() if not left_id: break left_seq = left.readline() left_plus = left.readline() left_quals = left.readline() # process the second file right_id = right.readline() right_seq = right.readline() right_plus = right.readline() right_quals = right.readline() if len(left_seq.strip()) <= args.rm_short_reads: continue if len(right_seq.strip()) <= args.rm_short_reads: continue # write output fout.write(left_id) fout.write(left_seq) fout.write(left_plus) fout.write(left_quals) fout.write(right_id) fout.write(right_seq) fout.write(right_plus) fout.write(right_quals) left.close() right.close() fout.close() return 0 if __name__ == '__main__': args = interface() process_reads(args)

Python: Interleave Paired-End Reads

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