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#!/usr/bin/env python3
"""Guess fastq quality encoding offset by checking the range
of the ASCII-encoded quality scores in FASTQ.
"""
import sys
import os.path
import signal
import subprocess
from argparse import ArgumentParser
cur = os.path.dirname(os.path.abspath(__file__))
sys.path.append(os.path.dirname(cur))
from dnapilib.io_utils import get_file_obj, fastq_quality
def guess_qual_offset(args):
platform = [ ('Sanger/Illumina-1.8+', 33, 76, 33),
('Illumina-1.5+', 67, 104, 64),
('Illumina-1.3+', 54, 104, 64),
('Solexa', 59, 104, 64) ]
q_chars = set()
fastqs = fastq_quality(get_file_obj(args.FASTQ))
sample_num = 50000
for i, quality in enumerate(fastqs):
if i == sample_num:
break
q_chars = q_chars.union(quality)
q_int = sorted(list(map(ord, q_chars)))
if len(q_int) <= 1:
raise Exception("unknown quality encoding")
for pl in platform:
if pl[1] <= q_int[1] and q_int[-2] <= pl[2]:
return "{}:base={}".format(pl[0], pl[3])
raise Exception("unknown quality encoding")
if __name__ == "__main__":
signal.signal(signal.SIGPIPE, signal.SIG_DFL)
prog = os.path.basename(sys.argv[0])
if sys.version_info.major <= 2:
raise ValueError("{} requires python version 3 or higher".format(prog))
parser = ArgumentParser(
description="Estimate quality score encoding")
parser.add_argument("FASTQ",
type=str,
help="including stdin or compressed file {zip,gz,tar,bz}")
args = parser.parse_args()
try:
print(guess_qual_offset(args))
except KeyboardInterrupt: pass
except Exception as e:
sys.exit(prog + ": error: " + str(e))
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