def _parse_single_genbank(chunks):
metadata = {}
interval_metadata = None
sequence = ''
# each section starts with a HEADER without indent.
section_splitter = _yield_section(lambda x: not x[0].isspace(),
strip=False)
for section in section_splitter(chunks):
header = section[0].split(None, 1)[0]
parser = _PARSER_TABLE.get(header, _parse_section_default)
if header == 'FEATURES':
# This requires 'LOCUS' line parsed before 'FEATURES', which should
# be true and is implicitly checked by the sniffer.
parser = partial(parser, length=metadata['LOCUS']['size'])
parsed = parser(section)
# reference can appear multiple times
if header == 'REFERENCE':
if header in metadata:
metadata[header].append(parsed)
else:
metadata[header] = [parsed]
elif header == 'ORIGIN':
sequence = parsed
elif header == 'FEATURES':
interval_metadata = parsed
else:
metadata[header] = parsed
return sequence, metadata, interval_metadata
def _parse_single_genbank(chunks):
metadata = {}
interval_metadata = None
sequence = ''
# each section starts with a HEADER without indent.
section_splitter = _yield_section(
lambda x: not x[0].isspace(), strip=False)
for section in section_splitter(chunks):
header = section[0].split(None, 1)[0]
parser = _PARSER_TABLE.get(
header, _parse_section_default)
if header == 'FEATURES':
# This requires 'LOCUS' line parsed before 'FEATURES', which should
# be true and is implicitly checked by the sniffer.
parser = partial(
parser, length=metadata['LOCUS']['size'])
parsed = parser(section)
# reference can appear multiple times
if header == 'REFERENCE':
if header in metadata:
metadata[header].append(parsed)
else:
metadata[header] = [parsed]
elif header == 'ORIGIN':
sequence = parsed
elif header == 'FEATURES':
interval_metadata = parsed
else:
metadata[header] = parsed
return sequence, metadata, interval_metadata
def _parse_reference(lines):
'''Parse single REFERENCE field.
'''
res = {}
# magic number 11: the non keyworded lines in REFERENCE
# are at least indented with 11 spaces.
feature_indent = ' ' * 11
section_splitter = _yield_section(
lambda x: not x.startswith(feature_indent),
skip_blanks=True, strip=False)
for section in section_splitter(lines):
label, data = _parse_section_default(
section, join_delimiter=' ', return_label=True)
res[label] = data
return res
def _parse_source(lines):
'''Parse SOURCE field.
'''
res = {}
# magic number 11: the non keyworded lines in SOURCE
# are at least indented with 11 spaces.
feature_indent = ' ' * 11
section_splitter = _yield_section(
lambda x: not x.startswith(feature_indent),
skip_blanks=True, strip=False)
# SOURCE line is not informative; skip it
_, organism = list(section_splitter(lines))
res['ORGANISM'] = organism[0].split(None, 1)[1].strip()
res['taxonomy'] = ' '.join([i.strip() for i in organism[1:]])
return res
