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#!/usr/bin/env python3
"""Clip off adapters from reads in FASTQ by searching kmer
exact prefix matches. There is an option '-s' that tries
to find prefix matches in length of (k + 1) nucleotides
with 1 mismatch if perfect prefix matches are not found.
After adapter removal, the program tallies clean reads
and writes non-redundant reads with the counts in FASTA.
"""
import sys
import re
import os.path
import signal
from operator import itemgetter
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_sequence
def make_regex(a_seq, a_len, is_3prime, sensitive):
if not a_seq:
return None, None
cutoff = a_len
if sensitive:
cutoff = a_len + 1
if len(a_seq) < cutoff:
message = "input adapters longer than {} nt"
raise Exception(message.format(cutoff-1))
a_seq = a_seq.upper().replace('U', 'T')
if is_3prime:
pat = "(.*)"
p_seq, m_seq = a_seq[:a_len], a_seq[:a_len+1]
beg, end = 0, a_len
else:
pat = "(.*?)"
p_seq, m_seq = a_seq[-a_len:], a_seq[-(a_len+1):]
beg, end = 1, a_len+1
pp = re.compile(pat+p_seq, re.IGNORECASE)
if not sensitive:
return pp, []
mp = []
seed = list(m_seq)
for i in range(beg, end):
ps = seed[:]
ps[i] = '.'
x = re.compile(pat+''.join(ps), re.IGNORECASE)
mp.append(x)
return pp, mp
def match_adapters(seq, pp, mps, sensitive, pi=0, mi=0, l=0):
if not pp:
return l, '*'
p = pp.search(seq)
if p:
return (p.end()-pi), '0'
if not sensitive:
return l, '*'
else:
for mp in mps:
m = mp.search(seq)
if m:
return (m.end()-mi), '1'
return l, '*'
def to_fasta(args):
if args.m <= 0:
raise Exception("bad value: -m")
if args.x <= 0:
raise Exception("bad value: -x")
if args.m == args.x:
raise Exception("bad read length cutoff range")
if not args.f and not args.b:
raise Exception("input adapter sequence")
if args.f == args.b:
raise Exception("5' and 3' adapters are same sequences")
if args.seed_5p <= 0:
raise Exception("bad value: --seed-5p")
if args.seed_3p <= 0:
raise Exception("bad value: --seed-3p")
if args.trim_3p < 0:
raise Exception("input positive value for 3'trimming")
if args.trim_5p < 0:
raise Exception("input positive value for 5'trimming")
f_seq, f_len = args.f, args.seed_5p
b_seq, b_len = args.b, args.seed_3p
if not f_seq and b_seq:
req = lambda x, y: y != '*' or args.a
elif f_seq and b_seq:
if args.B:
req = lambda x, y: x != '*' and y != '*' or args.a
else:
req = lambda x, y: x != '*' or y != '*' or args.a
elif f_seq and not b_seq:
req = lambda x, y: x != '*' or args.a
f_pp, f_mp = make_regex(f_seq, f_len, False, args.s)
b_pp, b_mp = make_regex(b_seq, b_len, True, args.s)
fas = {}
for seq in fastq_sequence(get_file_obj(args.FASTQ)):
seq_len = len(seq)
f_i, f_mm = match_adapters(seq, f_pp, f_mp, args.s)
b_i, b_mm = match_adapters(seq, b_pp, b_mp, args.s,
b_len, b_len+1, seq_len)
ins = seq[f_i+args.trim_5p : b_i-args.trim_3p]
ins_len = len(ins)
if req(f_mm, b_mm) and (args.m <= ins_len and ins_len <= args.x):
fas[ins] = fas.get(ins, 0) + 1
fas = sorted(fas.items(), key=itemgetter(0))
for seq, cnt in fas:
print(">{0}_{1}\n{0}".format(seq, cnt))
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="Remove adapters and collapse reads from FASTQ to FASTA")
parser.add_argument("FASTQ",
type=str,
help="including stdin or compressed file {zip,gz,tar,bz}")
parser.add_argument("-3",
metavar="SEQ",
dest="b",
help="3'adapter sequence")
parser.add_argument("-5",
metavar="SEQ",
dest="f",
help="5'adapter sequence")
parser.add_argument("--trim-5p",
metavar="BP",
type=int, default=0,
help="trim specified number of bases from 5'ends")
parser.add_argument("--trim-3p",
metavar="BP",
type=int, default=0,
help="trim specified number of bases from 3'ends")
parser.add_argument("--seed-5p",
metavar="BP",
type=int, default=7,
help="5' adapter match length in bp (default: %(default)s)")
parser.add_argument("--seed-3p",
metavar="BP",
type=int,default=7,
help="3' adapter match length in bp (default: %(default)s)")
parser.add_argument("-m",
metavar="BP",
type=int, default=16,
help="minimum read length in bp (default: %(default)s)")
parser.add_argument("-x",
metavar="BP",
type=int, default=36,
help="maximum read length in bp (default: %(default)s)")
parser.add_argument("-s",
action="store_true",
help="sensitive adapter search with 1 mismatch (default: off)")
parser.add_argument("-B",
action="store_true",
help="only print the reads with both 5' and 3' adapter matches")
parser.add_argument("-a",
action="store_true",
help="print all reads with and without adapter matches if the "
"reads are in the range specified with '-m' and '-x'")
args = parser.parse_args()
try:
to_fasta(args)
except KeyboardInterrupt: pass
except Exception as e:
sys.exit(prog + ": error: " + str(e))
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