1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
|
from __future__ import print_function
import os
from collections import Counter, defaultdict
from seqcluster.libs.classes import quality, umi
from itertools import product
import gzip
import re
import logging
logger = logging.getLogger('seqbuster')
def collapse(in_file):
"""collapse identical sequences and keep Q"""
keep = Counter()
with open_fastq(in_file) as handle:
line = handle.readline()
while line:
if line.startswith("@"):
if line.find("UMI_") > -1:
logger.info("Find UMI tags in read names, collapsing by UMI.")
return collapse_umi(in_file)
seq = handle.readline().strip()
handle.readline()
qual = handle.readline().strip()
if seq in keep:
keep[seq].update(qual)
else:
keep[seq] = quality(qual)
if line.startswith(">"):
seq = handle.readline().strip()
if seq not in keep:
keep[seq] = quality("".join(["I"] * len(seq)))
else:
keep[seq].update("".join(["I"] * len(seq)))
line = handle.readline()
logger.info("Sequences loaded: %s" % len(keep))
return keep
def collapse_umi(in_file):
"""collapse reads using UMI tags"""
keep = defaultdict(dict)
with open_fastq(in_file) as handle:
line = handle.readline();
while line:
if line.startswith("@"):
m = re.search('UMI_([ATGC]*)', line.strip())
umis = m.group(0)
seq = handle.readline().strip()
handle.readline()
qual = handle.readline().strip()
if (umis, seq) in keep:
keep[(umis, seq)][1].update(qual)
keep[(umis, seq)][0].update(seq)
else:
keep[(umis, seq)] = [umi(seq), quality(qual)]
line = handle.readline();
logger.info("Sequences loaded: %s" % len(keep))
return keep
def open_fastq(in_file):
""" open a fastq file, using gzip if it is gzipped
from bcbio package
"""
_, ext = os.path.splitext(in_file)
if ext == ".gz":
return gzip.open(in_file, 'rt')
if ext in [".fastq", ".fq", ".fasta", ".fa"]:
return open(in_file, 'r')
return ValueError("File needs to be fastq|fasta|fq|fa [.gz]")
def is_fastq(in_file):
"""copy from bcbio package"""
fastq_ends = [".txt", ".fq", ".fastq"]
zip_ends = [".gzip", ".gz"]
base, first_ext = os.path.splitext(in_file)
second_ext = os.path.splitext(base)[1]
if first_ext in fastq_ends:
return True
elif (second_ext, first_ext) in product(fastq_ends, zip_ends):
return True
else:
return False
def splitext_plus(f):
"""Split on file extensions, allowing for zipped extensions.
copy from bcbio
"""
base, ext = os.path.splitext(f)
if ext in [".gz", ".bz2", ".zip"]:
base, ext2 = os.path.splitext(base)
ext = ext2 + ext
return base, ext
def write_output(out_file, seqs, minimum=1, size=15):
idx =0
logger.info("Writing %s sequences to %s" % (len(seqs.keys()), out_file))
with open(out_file, 'w') as handle:
for s in seqs:
idx += 1
if isinstance(seqs[s], list):
seq = seqs[s][0].get()
qual = "".join(seqs[s][1].get())
counts = seqs[s][0].times
else:
seq = s
qual = "".join(seqs[s].get())
counts = seqs[s].times
if int(counts) >= minimum and len(seq) > size:
handle.write(("@seq_{idx}_x{counts}\n{seq}\n+\n{qual}\n").format(**locals()))
return out_file
|
