def parse_fast5_chunk(dn, cs, is_upper=False):
reads = []
n_seqs = 0
n_bases = 0
size = 0
f5s = [os.path.join(dn, f) for f in os.listdir(dn) if f.endswith(".fast5")]
for f5 in f5s:
f5h = lq_nanopore.open_fast5(f5)
top = lq_nanopore.list_toplevel(f5h)
for k in top:
if not k.startswith('read_'):
continue
fastq = lq_nanopore.get_fastq_from_multi_fast5(f5h, k).splitlines()
name = fastq[0].split(" ")[0]
if is_upper:
reads.append([name, fastq[1].upper(), fastq[3]])
else:
reads.append([name, fastq[1], fastq[3]])
size += sys.getsizeof(name) + sys.getsizeof(
fastq[1]) + sys.getsizeof(fastq[3])
n_bases += len(fastq[1])
n_seqs += 1
if size >= cs:
yield (reads, n_seqs, n_bases)
size = 0
reads = []
yield (reads, n_seqs, n_bases)
def guess_format(fn):
# assume fast5 is given in a dir.
if os.path.isdir(fn):
logger.info(
"not a file but a direcory %s is given. looking for fast5 files.."
% fn)
for f in os.listdir(fn):
if f.endswith(".fast5"):
f5 = lq_nanopore.open_fast5(os.path.join(fn, f))
if '/UniqueGlobalKey' in f5:
logger.error(
"single read fast5 is included? it's not supported for sampleqc."
)
return -1
return 4
logger.error("no fast5 is found.")
return -1
try:
fh = open(fn, 'rb')
except:
logger.error("cannot open %s" % fn)
try:
majic = os.read(fh.fileno(), 4)
except:
logger.error("cannot read %s" % fn)
# pybam and/or biopython way
if majic == 'BAM\1':
fh.close()
logger.debug("%s is an uncompressed BAM." % fn)
return 0
elif b'\x1f\x8b' in majic:
# YF memo: 1f 8b 08 04 code can exist in fq.gz either.
# changed the logic.
fh.close()
with gzip.open(fn, 'rb') as f:
l = f.read(4)
if "BAM" in l.decode(): # this should be 'BAM\x01'
logger.debug("%s is a compressed BAM." % fn)
return 0
else:
return __guess_sam_fastx(fn, isgzip=True)
else:
fh.close()
return __guess_sam_fastx(fn, isgzip=False)
def guess_format(fn):
# assume fast5 is given in a dir.
if os.path.isdir(fn):
logger.info(
"not a file but a direcory %s is given. looking for fast5 files.."
% fn)
for f in os.listdir(fn):
if f.endswith(".fast5"):
f5 = lq_nanopore.open_fast5(os.path.join(fn, f))
if '/UniqueGlobalKey' in f5:
logger.error(
"single read fast5 is included? it's not supported for sampleqc."
)
return -1
return 4
logger.error("no fast5 is found.")
return -1
try:
fh = open(fn, 'rb')
except:
logger.error("cannot open %s" % fn)
try:
majic = os.read(fh.fileno(), 4)
except:
logger.error("cannot read %s" % fn)
# pybam and/or biopython way
if majic == 'BAM\1':
return 0
fh.close()
elif majic == b'\x1f\x8b\x08\x04':
# compressed bam
return 0
fh.close()
fh.close()
try:
fh = open(fn, 'r')
except:
logger.error("cannot open %s" % fn)
# assume sam, fastx
at_line_cnt = 0
for line in fh:
if line[0] == '@':
at_line_cnt += 1
continue
elif at_line_cnt > 0:
if at_line_cnt > 1:
# header of sam
fh.close()
return 1
cn = len(line.split("\t"))
if cn == 11:
fh.close()
return 1
at_line_cnt = 0
# fastq
fh.close()
return 2
elif line[0] == '>' and at_line_cnt == 0:
# fasta
fh.close()
return 3
else:
cn = len(line.split("\t"))
if cn == 11:
fh.close()
return 1
at_line_cnt = 0
continue
# something else
fh.close()
return -1