def fasta_iter(handle, parse_description=True):
"""
Iterator over the given FASTA file handle, returning records. handle
is a handle to a file opened for reading
"""
line = handle.readline()
while line:
data = _screed_record_dict()
line = line.strip()
if not line.startswith('>'):
raise IOError("Bad FASTA format: no '>' at beginning of 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 = []
line = handle.readline()
while line and not line.startswith('>'):
sequenceList.append(line.strip())
line = handle.readline()
data['sequence'] = ''.join(sequenceList)
yield data
def fastq_iter(handle, line=None, parse_description=True):
"""
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 = line.strip()
while line:
data = _screed_record_dict()
if 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 = handle.readline().strip()
while not line.startswith('+') and not line.startswith('#'):
sequence.append(line)
line = handle.readline().strip()
data['sequence'] = ''.join(sequence)
# Extract the accuracy lines
accuracy = []
line = handle.readline().strip()
seqlen = len(data['sequence'])
aclen = 0
while not line == '' and aclen < seqlen:
accuracy.append(line)
aclen += len(line)
line = handle.readline().strip()
data['accuracy'] = ''.join(accuracy)
if len(data['sequence']) != len(data['accuracy']):
raise IOError('sequence and accuracy strings must be '\
'of equal length')
yield data
def fastq_iter(handle, line=None, parse_description=True):
"""
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 = line.strip()
while line:
data = _screed_record_dict()
if 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 = handle.readline().strip()
while not line.startswith('+') and not line.startswith('#'):
sequence.append(line)
line = handle.readline().strip()
data['sequence'] = ''.join(sequence)
# Extract the quality lines
quality = []
line = handle.readline().strip()
seqlen = len(data['sequence'])
aclen = 0
while not line == '' and aclen < seqlen:
quality.append(line)
aclen += len(line)
line = 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 data
def fasta_iter(handle, parse_description=True, line=None):
"""
Iterator over the given FASTA file handle, returning records. handle
is a handle to a file opened for reading
"""
if line is None:
line = handle.readline()
while line:
data = _screed_record_dict()
line = line.strip()
if not line.startswith('>'):
raise IOError("Bad FASTA format: no '>' at beginning of 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 = []
line = handle.readline()
while line and not line.startswith('>'):
sequenceList.append(line.strip())
line = handle.readline()
data['sequence'] = ''.join(sequenceList)
yield data
