def fastq_sort(fastq, byname=True, bysequence=False, tmpdir=None, chunksize=100000, out=sys.stdout, quiet=False):
tmpfiles = []
chunk = []
sys.stderr.write('Sorting FASTQ file into chunks...\n')
count = 0
for read in fastq.fetch(quiet):
count += 1
if byname:
chunk.append((read.name, read))
if bysequence:
chunk.append((read.seq, read))
if len(chunk) >= chunksize:
tmpfiles.append(_write_tmp(chunk))
chunk = []
if chunk:
tmpfiles.append(_write_tmp(chunk))
sys.stderr.write('Merging chunks...\n')
buf = [None, ] * len(tmpfiles)
skip = [False, ] * len(tmpfiles)
eta = ETA(count)
j=0
writing = True
while writing:
j+=1
eta.print_status(j)
for i, fobj in enumerate(tmpfiles):
if not buf[i] and not skip[i]:
try:
read = fastq_read_file(fobj)
if byname:
buf[i] = (read.name, i, read)
if bysequence:
buf[i] = (read.seq, i, read)
except:
buf[i] = None
skip[i] = True
sorted_list = buf[:]
sorted_list.sort()
writing = False
for tup in sorted_list:
if not tup:
continue
sorter, i, read = tup
read.write(out)
buf[i] = None
writing = True
break
eta.done()
def fastq_sort(fastq, bysequence=False, tmpdir=None, tmpprefix='.tmp', chunksize=100000, nogz=False, out=sys.stdout, quiet=False):
tmpfiles = []
chunk = []
sys.stderr.write('Sorting FASTQ file into chunks...\n')
count = 0
for read in fastq.fetch(quiet):
count += 1
if bysequence:
chunk.append((read.seq, read))
else:
chunk.append((read.name, read))
if len(chunk) >= chunksize:
tmpfiles.append(_write_tmp(chunk, tmpdir, tmpprefix, nogz))
chunk = []
if chunk:
tmpfiles.append(_write_tmp(chunk, tmpdir, tmpprefix, nogz))
sys.stderr.write('\nMerging chunks...\n')
sys.stderr.flush()
buf = [None, ] * len(tmpfiles)
skip = [False, ] * len(tmpfiles)
eta = ETA(count)
j=0
writing = True
if nogz:
tmpfobjs = [open(x) for x in tmpfiles]
else:
tmpfobjs = [gzip.open(x) for x in tmpfiles]
while writing:
j+=1
eta.print_status(j)
for i, fobj in enumerate(tmpfobjs):
if not buf[i] and not skip[i]:
try:
read = fastq_read_file(fobj)
if bysequence:
buf[i] = (read.seq, i, read)
else:
buf[i] = (read.name, i, read)
except:
buf[i] = None
skip[i] = True
sorted_list = buf[:]
sorted_list.sort()
writing = False
for tup in sorted_list:
if not tup:
continue
sorter, i, read = tup
read.write(out)
buf[i] = None
writing = True
break
eta.done()
for fobj in tmpfobjs:
fobj.close()
for tmpfile in tmpfiles:
os.unlink(tmpfile)
def fastq_sort(fastq,
bysequence=False,
tmpdir=None,
tmpprefix='.tmp',
chunksize=100000,
nogz=False,
out=sys.stdout,
quiet=False):
tmpfiles = []
chunk = []
sys.stderr.write('Sorting FASTQ file into chunks...\n')
count = 0
for read in fastq.fetch(quiet):
count += 1
if bysequence:
chunk.append((read.seq, read))
else:
chunk.append((read.name, read))
if len(chunk) >= chunksize:
tmpfiles.append(_write_tmp(chunk, tmpdir, tmpprefix, nogz))
chunk = []
if chunk:
tmpfiles.append(_write_tmp(chunk, tmpdir, tmpprefix, nogz))
sys.stderr.write('\nMerging chunks...\n')
sys.stderr.flush()
buf = [
None,
] * len(tmpfiles)
skip = [
False,
] * len(tmpfiles)
eta = ETA(count)
j = 0
writing = True
if nogz:
tmpfobjs = [open(x) for x in tmpfiles]
else:
tmpfobjs = [gzip.open(x) for x in tmpfiles]
while writing:
j += 1
eta.print_status(j)
for i, fobj in enumerate(tmpfobjs):
if not buf[i] and not skip[i]:
try:
read = fastq_read_file(fobj)
if bysequence:
buf[i] = (read.seq, i, read)
else:
buf[i] = (read.name, i, read)
except:
buf[i] = None
skip[i] = True
sorted_list = buf[:]
sorted_list.sort()
writing = False
for tup in sorted_list:
if not tup:
continue
sorter, i, read = tup
read.write(out)
buf[i] = None
writing = True
break
eta.done()
for fobj in tmpfobjs:
fobj.close()
for tmpfile in tmpfiles:
os.unlink(tmpfile)
