def test_from_reader(self):
scheme = GdcV1_0_0_ProtectedScheme()
lines = [
TestMafHeader.__version_line,
TestMafHeader.__annotation_line,
TestMafHeader.__sort_order_line,
]
reader = MafReader(
lines=lines,
validation_stringency=ValidationStringency.Silent,
scheme=scheme,
)
reader.close()
# No overrides
header = MafHeader.from_reader(reader=reader)
self.assertEqual(header.scheme().version(), scheme.version())
self.assertEqual(header.scheme().annotation_spec(),
scheme.annotation_spec())
self.assertEqual(header.sort_order().name(), Coordinate.name())
# Override version and annotation
scheme = GdcV1_0_0_PublicScheme()
header = MafHeader.from_reader(
reader=reader,
version=scheme.version(),
annotation=scheme.annotation_spec(),
sort_order=sort_order.Unsorted().name(),
)
self.assertEqual(header.scheme().version(), scheme.version())
self.assertEqual(header.scheme().annotation_spec(),
scheme.annotation_spec())
self.assertEqual(header.sort_order().name(),
sort_order.Unsorted().name())
def setup_maf_header(self):
"""
Sets up the maf header.
"""
# Reader header
_hdr = MafHeader.from_reader(reader=self.maf_reader)
if not self.options["reference_fasta_index"]:
self.maf_header = MafHeader.from_defaults(
version=self.options["version"],
annotation=self.options["annotation"],
sort_order=BarcodesAndCoordinate(),
contigs=_hdr.contigs(),
)
else:
self.maf_header = MafHeader.from_defaults(
version=self.options["version"],
annotation=self.options["annotation"],
sort_order=BarcodesAndCoordinate(),
fasta_index=self.options["reference_fasta_index"],
)
self.maf_header.validation_stringency = ValidationStringency.Strict
header_date = BaseRunner.get_header_date()
self.maf_header[header_date.key] = header_date
try:
nkey = _hdr["normal.aliquot"]
self.maf_header["normal.aliquot"] = nkey
except KeyError as e:
if not self.options["tumor_only"]:
raise e
tkey = _hdr["tumor.aliquot"]
self.maf_header["tumor.aliquot"] = tkey
def writer_from_reader(reader, options):
"""
Builds a writer from the given reader and command line options.
:param options: the command line options, which should have "output",
"version", and "annotation" defined.
:param reader: the reader from which to records will be obtained
:return:
"""
out_header = MafHeader.from_reader(
reader=reader,
version=options.version,
annotation=options.annotation,
sort_order=options.sort_order \
if hasattr(options, 'sort_order') else None
)
if options.output:
writer = MafWriter.from_path(
path=options.output,
header=out_header,
validation_stringency=options.validation_stringency)
else:
writer = MafWriter.from_fd(
desc=sys.stdout,
header=out_header,
validation_stringency=options.validation_stringency)
return writer
def setup_maf_header(self):
"""
Sets up the maf header.
"""
# Reader header
_hdr = MafHeader.from_reader(reader=self.maf_readers[0])
self.maf_header = MafHeader.from_defaults(
version=self.options['version'],
annotation=self.options['annotation'],
sort_order=BarcodesAndCoordinate(),
contigs=_hdr.contigs())
self.maf_header.validation_stringency = ValidationStringency.Strict
header_date = BaseRunner.get_header_date()
self.maf_header[header_date.key] = header_date
nkey = _hdr["normal.aliquot"]
self.maf_header["normal.aliquot"] = nkey
tkey = _hdr["tumor.aliquot"]
self.maf_header["tumor.aliquot"] = tkey
