def prepend_barcode(seqfile, bcfile, rc, text=''):
tmph = open(seqfile + '.tmp', 'w')
itr1 = FastqGeneralIterator(open(seqfile))
itr2 = FastqGeneralIterator(open(bcfile))
(h1, s1, q1) = itr1.next()
(h2, s2, q2) = itr2.next()
while 1:
h1 = h1.split()[0]
h2 = h2.split()[0]
while h1 != h2:
try:
(h2, s2, q2) = itr2.next()
h2 = h2.split()[0]
except (StopIteration, IOError):
break
if rc:
rcs = Seq(s2, generic_dna)
s2 = rcs.reverse_complement()
q2 = q2[::-1]
if text:
h1 = h1 + '.' + text
tmph.write("@%s\n%s%s\n+\n%s%s\n" % (h1, s2, s1, q2, q1))
try:
(h1, s1, q1) = itr1.next()
(h2, s2, q2) = itr2.next()
except (StopIteration, IOError):
break
tmph.close()
os.rename(seqfile + '.tmp', seqfile)
def prepend_barcode(seqfile, bcfile, rc, text=''):
tmph = open(seqfile+'.tmp', 'w')
itr1 = FastqGeneralIterator(open(seqfile))
itr2 = FastqGeneralIterator(open(bcfile))
(h1, s1, q1) = itr1.next()
(h2, s2, q2) = itr2.next()
while 1:
h1 = h1.split()[0]
h2 = h2.split()[0]
while h1 != h2:
try:
(h2, s2, q2) = itr2.next()
h2 = h2.split()[0]
except (StopIteration, IOError):
break
if rc:
rcs = Seq(s2, generic_dna)
s2 = rcs.reverse_complement()
q2 = q2[::-1]
if text:
h1 = h1+'.'+text
tmph.write("@%s\n%s%s\n+\n%s%s\n" %(h1, s2, s1, q2, q1))
try:
(h1, s1, q1) = itr1.next()
(h2, s2, q2) = itr2.next()
except (StopIteration, IOError):
break
tmph.close()
os.rename(seqfile+'.tmp', seqfile)
def main(args):
usage = "usage: %prog [options] -i <input index file> -s <input seq file> -o <output merge file>"+__doc__
parser = OptionParser(usage)
parser.add_option("-i", "--index", dest="index", default=None, help="Input index fastq file.")
parser.add_option("-s", "--seq", dest="seq", default=None, help="Input seq fastq file.")
parser.add_option("-o", "--output", dest="output", default=None, help="Output barcode file.")
(opts, args) = parser.parse_args()
if not (opts.index and os.path.isfile(opts.index) and opts.seq and os.path.isfile(opts.seq) and opts.output):
parser.error("Missing input and/or output")
outh = open(opts.output+'.tmp', 'w')
itr1 = FastqGeneralIterator(open(opts.seq))
itr2 = FastqGeneralIterator(open(opts.index))
(h1, s1, q1) = itr1.next()
(h2, s2, q2) = itr2.next()
while 1:
h1 = h1.split()[0]
h2 = h2.split()[0]
while h1 != h2:
try:
(h2, s2, q2) = itr2.next()
h2 = h2.split()[0]
except (StopIteration, IOError):
break
outh.write("@%s\n%s%s\n+\n%s%s\n" %(h1, s2, s1, q2, q1))
try:
(h1, s1, q1) = itr1.next()
(h2, s2, q2) = itr2.next()
except (StopIteration, IOError):
break
outh.close()
os.rename(opts.output+'.tmp', opts.output)
return 0
def main(args):
usage = "usage: %prog [options] -i <input index file> -s <input seq file> -o <output merge file>" + __doc__
parser = OptionParser(usage)
parser.add_option("-i",
"--index",
dest="index",
default=None,
help="Input index fastq file.")
parser.add_option("-s",
"--seq",
dest="seq",
default=None,
help="Input seq fastq file.")
parser.add_option("-o",
"--output",
dest="output",
default=None,
help="Output barcode file.")
(opts, args) = parser.parse_args()
if not (opts.index and os.path.isfile(opts.index) and opts.seq
and os.path.isfile(opts.seq) and opts.output):
parser.error("Missing input and/or output")
outh = open(opts.output + '.tmp', 'w')
itr1 = FastqGeneralIterator(open(opts.seq))
itr2 = FastqGeneralIterator(open(opts.index))
(h1, s1, q1) = itr1.next()
(h2, s2, q2) = itr2.next()
while 1:
h1 = h1.split()[0]
h2 = h2.split()[0]
while h1 != h2:
try:
(h2, s2, q2) = itr2.next()
h2 = h2.split()[0]
except (StopIteration, IOError):
break
outh.write("@%s\n%s%s\n+\n%s%s\n" % (h1, s2, s1, q2, q1))
try:
(h1, s1, q1) = itr1.next()
(h2, s2, q2) = itr2.next()
except (StopIteration, IOError):
break
outh.close()
os.rename(opts.output + '.tmp', opts.output)
return 0
def main():
count = 0
fnum = 1
if not paired:
handle = open( "%s_%03d.fq" % (arguments['--output'], fnum), "w")
for t,s,q in FastqGeneralIterator(open(arguments['<file.fastq>'], "r")):
if count >= arguments['--number']:
handle.close()
count = 0
fnum += 1
handle = open( "%s_%03d.fq" % (arguments['--output'], fnum), "w")
handle.write( "@%s\n%s\n+\n%s\n" % (t,s,q) )
count += 1
else:
#going to assume all reads are in both files and skip error checking
h1 = open( "%s_R1_%03d.fq" % (arguments['--output'], fnum), "w")
h2 = open( "%s_R2_%03d.fq" % (arguments['--output'], fnum), "w")
r2_gen = FastqGeneralIterator(open(arguments['<read2.fastq>'], "r"))
for t,s,q in FastqGeneralIterator(open(arguments['<file.fastq>'], "r")):
if count >= arguments['--number']:
h1.close()
h2.close()
count = 0
fnum += 1
h1 = open( "%s_R1_%03d.fq" % (arguments['--output'], fnum), "w")
h2 = open( "%s_R2_%03d.fq" % (arguments['--output'], fnum), "w")
h1.write( "@%s\n%s\n+\n%s\n" % (t,s,q) )
h2.write( "@%s\n%s\n+\n%s\n" % r2_gen.next() )
count += 1
def distribute_reads(readfiles, read_hit_dict, single=True):
iterator1 = FastqGeneralIterator(open(readfiles[0]))
if len(readfiles) == 1:
for ID1_long, Seq1, Qual1 in iterator1:
ID1 = ID1_long.split()[0]
if ID1 in read_hit_dict:
for target in read_hit_dict[ID1]:
write_single_seqs(target, ID1, Seq1)
return
elif len(readfiles) == 2:
iterator2 = FastqGeneralIterator(open(readfiles[1]))
for ID1_long, Seq1, Qual1 in iterator1:
ID2_long, Seq2, Qual2 = iterator2.next()
ID1 = ID1_long.split()[0]
ID2 = ID2_long.split()[0]
if ID1 in read_hit_dict:
for target in read_hit_dict[ID1]:
write_paired_seqs(target, ID1, Seq1, ID2, Seq2)
elif ID2 in read_hit_dict:
for target in read_hit_dict[ID2]:
write_paired_seqs(target, ID1, Seq1, ID2, Seq2)
def lookup_index_cycles(index_fn):
iterator = FastqGeneralIterator(gzip.open(args.index_read_file))
name, seq, qual = iterator.next()
return len(seq)
def distribute_reads(readfiles,read_hit_dict,single=True): iterator1 = FastqGeneralIterator(open(readfiles[0])) if len(readfiles) == 1: for ID1_long, Seq1, Qual1 in iterator1: ID1 = ID1_long.split()[0] if ID1 in read_hit_dict: for target in read_hit_dict[ID1]: write_single_seqs(target,ID1,Seq1) return elif len(readfiles) == 2: iterator2 = FastqGeneralIterator(open(readfiles[1])) for ID1_long, Seq1, Qual1 in iterator1: ID2_long, Seq2, Qual2 = iterator2.next() ID1 = ID1_long.split()[0] ID2 = ID2_long.split()[0] if ID1 in read_hit_dict: for target in read_hit_dict[ID1]: write_paired_seqs(target,ID1,Seq1,ID2,Seq2) elif ID2 in read_hit_dict: for target in read_hit_dict[ID2]: write_paired_seqs(target,ID1,Seq1,ID2,Seq2)
def stitch_seqs(outfile, file1, file2, blen):
bseq = 'N' * blen
bqual = '!' * blen
itr1 = FastqGeneralIterator(open(file1))
itr2 = FastqGeneralIterator(open(file2))
rec1 = itr1.next()
rec2 = itr2.next()
outh = open(outfile, 'w')
while 1:
seq2 = Seq(rec2[1], generic_dna)
outh.write("@%s\n%s%s%s\n+\n%s%s%s\n" %(rec1[0].split()[0], rec1[1], bseq, str(seq2.reverse_complement()), rec1[2], bqual, rec2[2][::-1]))
try:
rec1 = itr1.next()
rec2 = itr2.next()
except (StopIteration, IOError):
break
outh.close()
def stitch_seqs(outfile, file1, file2, blen):
bseq = 'N' * blen
bqual = '!' * blen
itr1 = FastqGeneralIterator(open(file1))
itr2 = FastqGeneralIterator(open(file2))
rec1 = itr1.next()
rec2 = itr2.next()
outh = open(outfile, 'w')
while 1:
seq2 = Seq(rec2[1], generic_dna)
outh.write(
"@%s\n%s%s%s\n+\n%s%s%s\n" %
(rec1[0].split()[0], rec1[1], bseq, str(
seq2.reverse_complement()), rec1[2], bqual, rec2[2][::-1]))
try:
rec1 = itr1.next()
rec2 = itr2.next()
except (StopIteration, IOError):
break
outh.close()
def parse_2fastq_parallel(file1, file2):
""" Parse two fastq files in parallel - generator yielding (name, seq1, seq2, qual1, qual2) tuples.
Doesn't check that the readnames match.
"""
from Bio.SeqIO.QualityIO import FastqGeneralIterator # Bio is the biopython package
with open(file1) as INFILE1:
with open(file2) as INFILE2:
generator1 = FastqGeneralIterator(INFILE1)
generator2 = FastqGeneralIterator(INFILE2)
if_finished_1, if_finished_2 = False, False
while True:
try: name1, seq1, qual1 = generator1.next()
except StopIteration: if_finished_1 = True
try: name2, seq2, qual2 = generator2.next()
except StopIteration: if_finished_2 = True
name = name1.split()[0]
if not if_finished_1 and not if_finished_2:
yield (name, seq1, seq2, qual1, qual2)
elif if_finished_1 and if_finished_2:
raise StopIteration
else:
raise DeepseqError("One file finished but the other one didn't! Read name %s"%(
name if if_finished_2 else name2.split()[0]))
if (args.read2_file != None):
iterator2 = FastqGeneralIterator(gzip.open(args.read2_file))
if (args.read3_file != None):
iterator3 = FastqGeneralIterator(gzip.open(args.read3_file))
func = None
if (args.mismatches > 0):
func = make_fuzzy_match(args.mismatches, args.n_penalty)
else:
func = make_strict_match(read_index_length, indexes)
for rname1, seq1, qual1 in FastqGeneralIterator(gzip.open(args.read1_file)):
rnamei, seqi, quali = iteratori.next()
out_index = func(seqi, indexes)
if (out_index is None):
out_index = 'unknown'
if (iterator2 is not None):
rname2, seq2, qual2 = iterator2.next()
if (iterator3 is not None):
rname3, seq3, qual3 = iterator3.next()
read3_index_out_fh[out_index].write('@' + rname3 + ":" + seq3 + "\n")
#read1_iter = SeqIO.parse(sys.argv[1], "fastq")
#read2_iter = SeqIO.parse(sys.argv[2], "fastq")
read1_iter = FastqGeneralIterator(open(sys.argv[1]))
read2_iter = FastqGeneralIterator(open(sys.argv[2]))
read1_out = open(sys.argv[3], 'w')
read2_out = open(sys.argv[4], 'w')
min_length = int(sys.argv[5])
max_length = int(sys.argv[6])
pairs_discarded = 0
for read1_id, read1_seq, read1_qual in read1_iter:
read2_id, read2_seq, read2_qual = read2_iter.next()
read1_seq = read1_seq[5:]
read1_qual = read1_qual[5:]
read2_seq = read2_seq[5:]
read2_qual = read2_qual[5:]
if len(read1_seq) < min_length or len(read2_seq) < min_length:
pairs_discarded += 1
continue
#SeqIO.write(read1, read1_out, "fastq")
#SeqIO.write(read2, read2_out, "fastq")
if len(read1_seq) > max_length:
read1_seq = read1_seq[:max_length]
read1_qual = read1_qual[:max_length]
else:
handle1 = open(fastq1)
if fastq2.endswith(".gz"):
sys.stderr.write("Decompressing %s\n" % fastq2)
handle2 = gzip.open(fastq2)
else:
handle2 = open(fastq2)
sys.stderr.write("Interlacing paired FASTQ files to stdout...\n")
out_handle = sys.stdout
iter1 = FastqGeneralIterator(handle1)
iter2 = FastqGeneralIterator(handle2)
for title1, seq1, qual1 in iter1:
try:
title2, seq2, qual2 = iter2.next()
except StopIteration:
sys_exit("More records in %s than %s, e.g. %s" %
(fastq1, fastq2, title1))
id1, descr1 = title1.split(None, 1)
id2, descr2 = title2.split(None, 1)
if id1 == id2:
# Add the /1 and /2, preserve any description after the ID
if descr1:
descr1 = " " + descr1
if descr2:
descr2 = " " + descr2
out_handle.write("@%s/1%s\n%s\n+\n%s\n@%s/2%s\n%s\n+\n%s\n"
% (id1, descr1, seq1, qual1, id2, descr2, seq2, qual2))
elif id1.endswith("/1") and id2.endswith("/2") and id1[:-2] == id2[:-2]:
out_handle.write("@%s\n%s\n+\n%s\n@%s\n%s\n+\n%s\n"
#!/usr/bin/python
import sys
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.SeqIO.QualityIO import FastqGeneralIterator
#read1_iter = SeqIO.parse(sys.argv[1], "fastq")
#read2_iter = SeqIO.parse(sys.argv[2], "fastq")
read1_iter = FastqGeneralIterator(open(sys.argv[1]))
read2_iter = FastqGeneralIterator(open(sys.argv[2]))
kv_out_file = open(sys.argv[1] + ".tmp", "w")
for read1 in read1_iter:
read2 = read2_iter.next()
print(read1[0])
# strip off the /1 in read1 - this will be the key for the MR data file
read_id = read1[0][:len(read1[0]) - 2]
kv_out_file.write("\t".join([
read_id, read1[0], read1[1], read1[2], read2[0], read2[1], read2[2]
]) + "\n")
