def _parse_fasta_raw(fh, data_parser, format_label):
"""Raw parser for FASTA or QUAL files.
Returns raw values (seq/qual, id, description). It is the responsibility of
the caller to construct the correct in-memory object to hold the data.
"""
line = next(fh)
# header check inlined here and below for performance
if line.startswith('>'):
id_, desc = _parse_fasta_like_header(line)
else:
raise FASTAFormatError(
"Found line without a header in %s-formatted file:\n%s" %
(format_label, line))
data_chunks = []
for line in fh:
if line.startswith('>'):
# new header, so yield current record and reset state
yield data_parser(data_chunks), id_, desc
data_chunks = []
id_, desc = _parse_fasta_like_header(line)
else:
line = line.strip()
if line:
data_chunks.append(line)
else:
raise FASTAFormatError(
"Found blank or whitespace-only line in %s-formatted "
"file." % format_label)
# yield last record in file
yield data_parser(data_chunks), id_, desc
def _parse_fasta_raw(fh, data_parser, format_label):
"""Raw parser for FASTA or QUAL files.
Returns raw values (seq/qual, id, description). It is the responsibility of
the caller to construct the correct in-memory object to hold the data.
"""
line = next(fh)
# header check inlined here and below for performance
if line.startswith('>'):
id_, desc = _parse_fasta_like_header(line)
else:
raise FASTAFormatError(
"Found line without a header in %s-formatted file:\n%s" %
(format_label, line))
data_chunks = []
for line in fh:
if line.startswith('>'):
# new header, so yield current record and reset state
yield data_parser(data_chunks), id_, desc
data_chunks = []
id_, desc = _parse_fasta_like_header(line)
else:
line = line.strip()
if line:
data_chunks.append(line)
else:
raise FASTAFormatError(
"Found blank or whitespace-only line in %s-formatted "
"file." % format_label)
# yield last record in file
yield data_parser(data_chunks), id_, desc
def _fastq_to_generator(fh, variant=None, phred_offset=None,
constructor=Sequence):
# Skip any blank or whitespace-only lines at beginning of file
seq_header = next(_line_generator(fh, skip_blanks=True))
if not seq_header.startswith('@'):
raise FASTQFormatError(
"Expected sequence (@) header line at start of file: %r"
% seq_header)
while seq_header is not None:
id_, desc = _parse_fasta_like_header(seq_header)
seq, qual_header = _parse_sequence_data(fh, seq_header)
if qual_header != '+' and qual_header[1:] != seq_header[1:]:
raise FASTQFormatError(
"Sequence (@) and quality (+) header lines do not match: "
"%r != %r" % (seq_header[1:], qual_header[1:]))
phred_scores, seq_header = _parse_quality_scores(fh, len(seq),
variant,
phred_offset,
qual_header)
yield constructor(seq, metadata={'id': id_, 'description': desc},
positional_metadata={'quality': phred_scores})
def _fastq_to_generator(fh, variant=None, phred_offset=None,
constructor=Sequence, **kwargs):
# Skip any blank or whitespace-only lines at beginning of file
seq_header = next(_line_generator(fh, skip_blanks=True))
if not seq_header.startswith('@'):
raise FASTQFormatError(
"Expected sequence (@) header line at start of file: %r"
% seq_header)
while seq_header is not None:
id_, desc = _parse_fasta_like_header(seq_header)
seq, qual_header = _parse_sequence_data(fh, seq_header)
if qual_header != '+' and qual_header[1:] != seq_header[1:]:
raise FASTQFormatError(
"Sequence (@) and quality (+) header lines do not match: "
"%r != %r" % (seq_header[1:], qual_header[1:]))
phred_scores, seq_header = _parse_quality_scores(fh, len(seq),
variant,
phred_offset,
qual_header)
yield constructor(seq, metadata={'id': id_, 'description': desc},
positional_metadata={'quality': phred_scores},
**kwargs)
def _parse_fasta_raw(fh, data_parser, format_label):
"""Raw parser for FASTA or QUAL files.
Returns raw values (seq/qual, id, description). It is the responsibility of
the caller to construct the correct in-memory object to hold the data.
"""
# Skip any blank or whitespace-only lines at beginning of file
seq_header = next(_line_generator(fh, skip_blanks=True))
# header check inlined here and below for performance
if seq_header.startswith('>'):
id_, desc = _parse_fasta_like_header(seq_header)
else:
raise FASTAFormatError(
"Found non-header line when attempting to read the 1st %s record:"
"\n%s" % (format_label, seq_header))
data_chunks = []
prev = seq_header
for line in _line_generator(fh, skip_blanks=False):
if line.startswith('>'):
# new header, so yield current record and reset state
yield data_parser(data_chunks), id_, desc
data_chunks = []
id_, desc = _parse_fasta_like_header(line)
else:
if line:
# ensure no blank lines within a single record
if not prev:
raise FASTAFormatError(
"Found blank or whitespace-only line within %s "
"record." % format_label)
data_chunks.append(line)
prev = line
# yield last record in file
yield data_parser(data_chunks), id_, desc
def _parse_fasta_raw(fh, data_parser, error_type):
"""Raw parser for FASTA or QUAL files.
Returns raw values (seq/qual, id, description). It is the responsibility of
the caller to construct the correct in-memory object to hold the data.
"""
# Skip any blank or whitespace-only lines at beginning of file
seq_header = next(_line_generator(fh, skip_blanks=True))
# header check inlined here and below for performance
if seq_header.startswith('>'):
id_, desc = _parse_fasta_like_header(seq_header)
else:
raise error_type(
"Found non-header line when attempting to read the 1st record:"
"\n%s" % seq_header)
data_chunks = []
prev = seq_header
for line in _line_generator(fh, skip_blanks=False):
if line.startswith('>'):
# new header, so yield current record and reset state
yield data_parser(data_chunks), id_, desc
data_chunks = []
id_, desc = _parse_fasta_like_header(line)
else:
if line:
# ensure no blank lines within a single record
if not prev:
raise error_type(
"Found blank or whitespace-only line within record.")
data_chunks.append(line)
prev = line
# yield last record in file
yield data_parser(data_chunks), id_, desc
def _fastq_to_generator(fh, variant=None, phred_offset=None,
constructor=BiologicalSequence):
seq_header = next(_line_generator(fh))
if not seq_header.startswith('@'):
raise FASTQFormatError(
"Expected sequence (@) header line at start of file: %r"
% seq_header)
while seq_header is not None:
id_, desc = _parse_fasta_like_header(seq_header)
seq, qual_header = _parse_sequence_data(fh)
if qual_header != '+' and qual_header[1:] != seq_header[1:]:
raise FASTQFormatError(
"Sequence (@) and quality (+) header lines do not match: "
"%r != %r" % (seq_header[1:], qual_header[1:]))
phred_scores, seq_header = _parse_quality_scores(fh, len(seq), variant,
phred_offset)
yield constructor(seq, id=id_, description=desc, quality=phred_scores)
def _fastq_to_generator(fh,
variant=None,
phred_offset=None,
constructor=BiologicalSequence):
seq_header = next(_line_generator(fh))
if not seq_header.startswith('@'):
raise FASTQFormatError(
"Expected sequence (@) header line at start of file: %r" %
seq_header)
while seq_header is not None:
id_, desc = _parse_fasta_like_header(seq_header)
seq, qual_header = _parse_sequence_data(fh)
if qual_header != '+' and qual_header[1:] != seq_header[1:]:
raise FASTQFormatError(
"Sequence (@) and quality (+) header lines do not match: "
"%r != %r" % (seq_header[1:], qual_header[1:]))
phred_scores, seq_header = _parse_quality_scores(
fh, len(seq), variant, phred_offset)
yield constructor(seq, id=id_, description=desc, quality=phred_scores)
def test_id_and_description(self):
obs = _parse_fasta_like_header('>!thus suht! \t\t \n')
self.assertEqual(obs, ('!thus', 'suht!'))
def test_description_only(self):
obs = _parse_fasta_like_header('> suht! \t\t \n')
self.assertEqual(obs, ('', 'suht!'))
def test_id_only(self):
obs = _parse_fasta_like_header('>suht! \t\t \n')
self.assertEqual(obs, ('suht!', ''))
def test_no_id_or_description(self):
obs = _parse_fasta_like_header('> \t\t \n')
self.assertEqual(obs, ('', ''))
def test_id_and_description(self):
obs = _parse_fasta_like_header('>!thus suht! \t\t \n')
self.assertEqual(obs, ('!thus', 'suht!'))
def test_description_only(self):
obs = _parse_fasta_like_header('> suht! \t\t \n')
self.assertEqual(obs, ('', 'suht!'))
def test_id_only(self):
obs = _parse_fasta_like_header('>suht! \t\t \n')
self.assertEqual(obs, ('suht!', ''))
def test_no_id_or_description(self):
obs = _parse_fasta_like_header('> \t\t \n')
self.assertEqual(obs, ('', ''))
