def my_fastq_iter(handle, line=None, parse_description=False):
"""
Iterator over the given FASTQ file handle returning records. handle
is a handle to a file opened for reading
CTB: this relies on each FASTQ record being exactly 4 lines.
"""
while 1:
pos = handle.tell()
line = handle.readline()
if not line:
return
assert line.startswith('@'), line
name = to_str(line.strip())[1:]
line = handle.readline()
sequence = to_str(line.strip())
line = handle.readline()
plus = to_str(line.strip())
assert plus == '+'
line = handle.readline()
quality = to_str(line.strip())
yield Record(name, sequence, quality=quality), pos
def my_fastq_iter(handle, line=None, parse_description=False):
"""
Iterator over the given FASTQ file handle returning records. handle
is a handle to a file opened for reading
"""
if line is None:
line = handle.readline()
line = to_str(line.strip())
while line:
data = {}
if line and not line.startswith('@'):
raise IOError("Bad FASTQ format: no '@' at beginning of line")
# Try to grab the name and (optional) annotations
if parse_description:
try:
data['name'], data['annotations'] = line[1:].split(' ', 1)
except ValueError: # No optional annotations
data['name'] = line[1:]
data['annotations'] = ''
pass
else:
data['name'] = line[1:]
data['annotations'] = ''
# Extract the sequence lines
sequence = []
line = to_str(handle.readline().strip())
while line and not line.startswith('+') and not line.startswith('#'):
sequence.append(line)
line = to_str(handle.readline().strip())
data['sequence'] = ''.join(sequence)
# Extract the quality lines
quality = []
line = to_str(handle.readline().strip())
seqlen = len(data['sequence'])
aclen = 0
while not line == '' and aclen < seqlen:
quality.append(line)
aclen += len(line)
line = to_str(handle.readline().strip())
data['quality'] = ''.join(quality)
if len(data['sequence']) != len(data['quality']):
raise IOError('sequence and quality strings must be '
'of equal length')
yield Record(**data)
def my_fastq_iter(handle, line=None, parse_description=False):
"""
Iterator over the given FASTQ file handle returning records. handle
is a handle to a file opened for reading
"""
if line is None:
line = handle.readline()
line = to_str(line.strip())
while line:
data = {}
if line and not line.startswith('@'):
raise IOError("Bad FASTQ format: no '@' at beginning of line")
# Try to grab the name and (optional) annotations
if parse_description:
try:
data['name'], data['annotations'] = line[1:].split(' ', 1)
except ValueError: # No optional annotations
data['name'] = line[1:]
data['annotations'] = ''
pass
else:
data['name'] = line[1:]
data['annotations'] = ''
# Extract the sequence lines
sequence = []
line = to_str(handle.readline().strip())
while line and not line.startswith('+') and not line.startswith('#'):
sequence.append(line)
line = to_str(handle.readline().strip())
data['sequence'] = ''.join(sequence)
# Extract the quality lines
quality = []
line = to_str(handle.readline().strip())
seqlen = len(data['sequence'])
aclen = 0
while not line == '' and aclen < seqlen:
quality.append(line)
aclen += len(line)
line = to_str(handle.readline().strip())
data['quality'] = ''.join(quality)
if len(data['sequence']) != len(data['quality']):
raise IOError('sequence and quality strings must be '
'of equal length')
yield Record(**data)
def my_fasta_iter(handle, parse_description=False, line=None):
"""
Iterator over the given FASTA file handle, returning records. handle
is a handle to a file opened for reading
"""
last_start = handle.tell()
if line is None:
line = handle.readline()
while line:
data = {}
line = to_str(line.strip())
if not line.startswith('>'):
raise IOError(
"Bad FASTA format: no '>' at beginning of line: {}".format(
line))
if parse_description: # Try to grab the name and optional description
try:
data['name'], data['description'] = line[1:].split(' ', 1)
except ValueError: # No optional description
data['name'] = line[1:]
data['description'] = ''
else:
data['name'] = line[1:]
data['description'] = ''
data['name'] = data['name'].strip()
data['description'] = data['description'].strip()
# Collect sequence lines into a list
sequenceList = []
pos = handle.tell()
line = to_str(handle.readline())
while line and not line.startswith('>'):
sequenceList.append(line.strip())
pos = handle.tell()
line = to_str(handle.readline())
data['sequence'] = ''.join(sequenceList)
yield Record(**data), last_start
last_start = pos
def my_fasta_iter(handle, parse_description=False, line=None):
"""
Iterator over the given FASTA file handle, returning records. handle
is a handle to a file opened for reading
"""
last_start = handle.tell()
if line is None:
line = handle.readline()
while line:
data = {}
line = to_str(line.strip())
if not line.startswith('>'):
raise IOError("Bad FASTA format: no '>' at beginning of line: {}".format(line))
if parse_description: # Try to grab the name and optional description
try:
data['name'], data['description'] = line[1:].split(' ', 1)
except ValueError: # No optional description
data['name'] = line[1:]
data['description'] = ''
else:
data['name'] = line[1:]
data['description'] = ''
data['name'] = data['name'].strip()
data['description'] = data['description'].strip()
# Collect sequence lines into a list
sequenceList = []
pos = handle.tell()
line = to_str(handle.readline())
while line and not line.startswith('>'):
sequenceList.append(line.strip())
pos = handle.tell()
line = to_str(handle.readline())
data['sequence'] = ''.join(sequenceList)
yield Record(**data), last_start
last_start = pos
