Reverse a qual score file. May be needed when trying to match up reverse complemented fasta files.

reverse_qual_scores.py

#!/usr/bin/env python

""" Used to reverse a qual score sequence, which may be needed in cases of 
paired fasta/qual files.

Requires QIIME installed to use (created with 1.7.0dev)

Usage:
python reverse_qual_scores.py X Y
where X is qual scores filepath, Y is output reversed filepath
"""

from sys import argv

from qiime.parse import MinimalQualParser
from qiime.split_libraries import format_qual_output

input_qual = open(argv[1], "U")

output_qual = open(argv[2], "w")

for label, seq in MinimalQualParser(input_qual, full_header=True):
    output_qual.write(">%s\n%s" % (label, format_qual_output(seq[::-1])))