def start_trim(f, lock, conn, args):
'''Start the actual trimming of a file'''
if args.gz: fh = gzip.open(f, 'rb')
else: fh = open(f, 'r')
# set adaptors #
adaptors = set_adaptors(args.adaptors, args.min_adaptor_match)
# set fqtype #
format = genobox_modules.set_filetype(f, args.gz)
if format == 'fastq': fqtype = genobox_modules.set_fqtype(f, args.gz)
else: raise ValueError('Input not fastq\n')
# start trimming file #
total = 0
written = 0
for (title, sequence, quality) in FastqGeneralIterator(fh):
#lock.acquire()
total += 1
(title, sequence, quality) = filter_adaptor(adaptors, args.min_adaptor_match, args.min_length, title, sequence, quality)
(title, sequence, quality) = trim_qual(args.min_baseq, args.min_avgq, args.min_length, fqtype, title, sequence, quality)
if title != None:
if len(sequence) != len(quality):
raise ValueError('sequence and quality not of the same length\n%s\n%s\n' % (sequence, quality))
written += 1
conn.send('@%s\n%s\n+\n%s\n' % (title, sequence, quality))
#lock.release()
conn.send('Stop')
conn.close()
return written, total
def check_formats_fq(i, gz, bwa6):
'''Checks format of fastq file and returns it'''
import genobox_modules
# check if fastq and if so mode
format = genobox_modules.set_filetype(i, gz)
if format != 'fastq':
raise ValueError('Input must be fastq')
else:
fqtype = genobox_modules.set_fqtype(i, gz)
return fqtype
def check_formats_fq(i, gz, bwa6):
'''Checks format of fastq file and returns it'''
import genobox_modules
# check if fastq and if so mode
format = genobox_modules.set_filetype(i, gz)
if format != 'fastq':
raise ValueError('Input must be fastq')
else:
fqtype = genobox_modules.set_fqtype(i, gz)
return fqtype
def start_trim(f, lock, conn, args):
'''Start the actual trimming of a file'''
if args.gz: fh = gzip.open(f, 'rb')
else: fh = open(f, 'r')
# set adaptors #
adaptors = set_adaptors(args.adaptors, args.min_adaptor_match)
# set fqtype #
format = genobox_modules.set_filetype(f, args.gz)
if format == 'fastq': fqtype = genobox_modules.set_fqtype(f, args.gz)
else: raise ValueError('Input not fastq\n')
# start trimming file #
total = 0
written = 0
for (title, sequence, quality) in FastqGeneralIterator(fh):
#lock.acquire()
total += 1
(title, sequence,
quality) = filter_adaptor(adaptors, args.min_adaptor_match,
args.min_length, title, sequence,
quality)
(title, sequence, quality) = trim_qual(args.min_baseq,
args.min_avgq,
args.min_length, fqtype,
title, sequence, quality)
if title != None:
if len(sequence) != len(quality):
raise ValueError(
'sequence and quality not of the same length\n%s\n%s\n'
% (sequence, quality))
written += 1
conn.send('@%s\n%s\n+\n%s\n' % (title, sequence, quality))
#lock.release()
conn.send('Stop')
conn.close()
return written, total
def __init__(self, f, o, l=25, q=20, m=20, keep_n=False, M=20,
a=['GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG', 'ACACTCTTTCCCTACACGACGCTCTTCCGATCT',
'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT',
'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT',
'CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT',
'ACACTCTTTCCCTACACGACGCTCTTCCGATCT'], gz=False):
self.f = f
self.o = o
self.l = l
self.q = q
self.m = m
self.keep_n = keep_n
self.M = M
self.a = a
self.paired = False
self.interleaved = False
self.gz = gz
# set adaptors, readtype, fastq format
self.adaptors = self.set_adaptors()
self.set_readtype()
self.format = genobox_modules.set_filetype(self.f[0], self.gz)
if self.format == 'fastq':
self.fqtype = genobox_modules.set_fqtype(self.f[0], self.gz)
def __init__(
self,
f,
o,
l=25,
q=20,
m=20,
keep_n=False,
M=20,
a=[
'GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG',
'ACACTCTTTCCCTACACGACGCTCTTCCGATCT',
'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT',
'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT',
'CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT',
'ACACTCTTTCCCTACACGACGCTCTTCCGATCT'
],
gz=False):
self.f = f
self.o = o
self.l = l
self.q = q
self.m = m
self.keep_n = keep_n
self.M = M
self.a = a
self.paired = False
self.interleaved = False
self.gz = gz
# set adaptors, readtype, fastq format
self.adaptors = self.set_adaptors()
self.set_readtype()
self.format = genobox_modules.set_filetype(self.f[0], self.gz)
if self.format == 'fastq':
self.fqtype = genobox_modules.set_fqtype(self.f[0], self.gz)
