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 setup_maf_header(self):
"""
Sets up the maf header.
"""
self.maf_header = MafHeader.from_defaults(
version=self.options["version"],
annotation=self.options["annotation"],
sort_order=BarcodesAndCoordinate(),
fasta_index=self.options["reference_fasta_index"],
)
header_date = BaseRunner.get_header_date()
self.maf_header[header_date.key] = header_date
if not self.options["tumor_only"]:
normal_aliquot = MafHeaderRecord(
key="normal.aliquot",
value=self.options["normal_aliquot_uuid"]
if not self.options["tumor_only"]
else "",
)
self.maf_header[normal_aliquot.key] = normal_aliquot
tumor_aliquot = MafHeaderRecord(
key="tumor.aliquot", value=self.options["tumor_aliquot_uuid"]
)
self.maf_header[tumor_aliquot.key] = tumor_aliquot
def test_from_defaults(self):
header = MafHeader.from_defaults(
version=TestMafHeader.Scheme.version(),
annotation=TestMafHeader.Scheme.annotation_spec(),
sort_order=Coordinate(),
)
self.assertIsNotNone(header.scheme())
self.assertIsNotNone(header.scheme().version())
self.assertIsNotNone(header.scheme().annotation_spec())
self.assertIsNotNone(header.sort_order())
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
