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
|
import os
from seqcluster.libs.fastq import collapse, splitext_plus, write_output, open_fastq
import logging
logger = logging.getLogger('seqbuster')
def collapse_fastq(args):
"""collapse fasq files after adapter trimming
"""
try:
umi_fn = args.fastq
if _is_umi(args.fastq):
umis = collapse(args.fastq)
umi_fn = os.path.join(args.out, splitext_plus(os.path.basename(args.fastq))[0] + "_umi_trimmed.fastq")
write_output(umi_fn, umis, args.minimum)
seqs = collapse(umi_fn)
out_file = splitext_plus(os.path.basename(args.fastq))[0] + "_trimmed.fastq"
except IOError as e:
logger.error("I/O error({0}): {1}".format(e.errno, e.strerror))
raise "Can not read file"
out_file = os.path.join(args.out, out_file)
write_output(out_file, seqs, args.minimum)
return out_file
def _is_umi(fn):
with open_fastq(fn) as inh:
if inh.readline().find("UMI_") > -1:
return True
return False
|
