parse_fastqc.py

#!/usr/bin/env python3

import sys

with open(sys.argv[1], "r") as fqc:
    line = fqc.readline()
    assert line.startswith("##FastQC")
    while not line.startswith(">>Overrepresented sequences"):
        line = fqc.readline()
    seq, count, percent, source = fqc.readline().strip().split("\t")
    assert seq == "#Sequence"
    #cumul_percent = 0
    line = fqc.readline()
    order = 0
    while not line.startswith(">>END_MODULE"):
        seq, _, percent, _ = line.strip().split("\t")
        order += 1
        #cumul_percent += float(percent)
        print(">Over_represented_%d (%s)\n%s" % (order, percent, seq))
        line = fqc.readline()

sys.exit(0)