def reference_genome(self):
"""Reference genome.
Returns
-------
:class:`.ReferenceGenome`
Reference genome.
"""
if self._rg is None:
self._rg = hl.default_reference()
return self._rg
def values(self):
values = [
(hl.tbool, True),
(hl.tint32, 0),
(hl.tint64, 0),
(hl.tfloat32, 0.5),
(hl.tfloat64, 0.5),
(hl.tstr, "foo"),
(hl.tstruct(x=hl.tint32), hl.Struct(x=0)),
(hl.tarray(hl.tint32), [0, 1, 4]),
(hl.tset(hl.tint32), {0, 1, 4}),
(hl.tdict(hl.tstr, hl.tint32), {"a": 0, "b": 1, "c": 4}),
(hl.tinterval(hl.tint32), hl.Interval(0, 1, True, False)),
(hl.tlocus(hl.default_reference()), hl.Locus("1", 1)),
(hl.tcall, hl.Call([0, 1]))
]
return values
def vep_or_lookup_vep(ht,
reference_vep_ht=None,
reference=None,
vep_config=None):
"""
VEP a table, or lookup variants in a reference database
:param ht: Input Table
:param reference_vep_ht: A reference database with VEP annotations (must be in top-level `vep`)
:param reference: If reference_vep_ht is not specified, find a suitable one in reference (if None, grabs from hl.default_reference)
:param vep_config: vep_config to pass to hl.vep (if None, a suitable one for `reference` is chosen)
:return: VEPped Table
"""
if reference is None:
reference = hl.default_reference().name
if reference_vep_ht is None:
possible_refs = ("GRCh37", "GRCh38")
if reference not in possible_refs:
raise ValueError(
f'vep_or_lookup_vep got {reference}. Expected one of {", ".join(possible_refs)}'
)
reference_vep_ht = hl.read_table(vep_context_ht_path(reference))
ht = ht.annotate(vep=reference_vep_ht[ht.key].vep)
vep_ht = ht.filter(hl.is_defined(ht.vep))
revep_ht = ht.filter(hl.is_missing(ht.vep))
if vep_config is None:
vep_config = vep_config_path(reference)
revep_ht = hl.vep(revep_ht, vep_config)
return vep_ht.union(revep_ht)
def get_r_within_gene(bm: BlockMatrix,
ld_index: hl.Table,
gene: str,
vep_ht: hl.Table = None,
reference_genome: str = None):
"""
Gets LD information (`r`) for all pairs of variants within `gene`.
Warning: this returns a table quadratic in number of variants. Exercise caution with large genes.
:param bm: Input Block Matrix
:param ld_index: Corresponding index table
:param gene: Gene symbol as string
:param vep_ht: Table with VEP annotations (if None, gets from get_gnomad_public_data())
:param reference_genome: Reference genome to pass to get_gene_intervals for fast filtering to gene
:return: Table with pairs of variants
"""
if vep_ht is None:
vep_ht = public_release('exomes').ht()
if reference_genome is None:
reference_genome = hl.default_reference().name
intervals = hl.experimental.get_gene_intervals(
gene_symbols=[gene], reference_genome=reference_genome)
ld_index = hl.filter_intervals(ld_index, intervals)
ld_index = ld_index.annotate(vep=vep_ht[ld_index.key].vep)
ld_index = ld_index.filter(
hl.any(lambda tc: tc.gene_symbol == gene,
ld_index.vep.transcript_consequences))
indices_to_keep = ld_index.idx.collect()
filt_bm = bm.filter(indices_to_keep, indices_to_keep)
ht = filt_bm.entries()
ld_index = ld_index.add_index('new_idx').key_by('new_idx')
return ht.transmute(r=ht.entry,
i_variant=ld_index[ht.i],
j_variant=ld_index[ht.j])
def get_gene_intervals(gene_symbols=None,
gene_ids=None,
transcript_ids=None,
verbose=True,
reference_genome=None,
gtf_file=None):
"""Get intervals of genes or transcripts.
Get the boundaries of genes or transcripts from a GTF file, for quick filtering of a Table or MatrixTable.
On Google Cloud platform:
Gencode v19 (GRCh37) GTF available at: gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz
Gencode v29 (GRCh38) GTF available at: gs://hail-common/references/gencode/gencode.v29.annotation.gtf.bgz
Example
-------
>>> hl.filter_intervals(ht, get_gene_intervals(gene_symbols=['PCSK9'], reference_genome='GRCh37')) # doctest: +SKIP
Parameters
----------
gene_symbols : :obj:`list` of :obj:`str`, optional
Gene symbols (e.g. PCSK9).
gene_ids : :obj:`list` of :obj:`str`, optional
Gene IDs (e.g. ENSG00000223972).
transcript_ids : :obj:`list` of :obj:`str`, optional
Transcript IDs (e.g. ENSG00000223972).
verbose : :obj:`bool`
If ``True``, print which genes and transcripts were matched in the GTF file.
reference_genome : :obj:`str` or :class:`.ReferenceGenome`, optional
Reference genome to use (passed along to import_gtf).
gtf_file : :obj:`str`
GTF file to load. If none is provided, but `reference_genome` is one of
`GRCh37` or `GRCh38`, a default will be used (on Google Cloud Platform).
Returns
-------
:obj:`list` of :class:`.Interval`
"""
GTFS = {
'GRCh37':
'gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz',
'GRCh38':
'gs://hail-common/references/gencode/gencode.v29.annotation.gtf.bgz',
}
if reference_genome is None:
reference_genome = hl.default_reference().name
else:
reference_genome = reference_genome.name
if gtf_file is None:
gtf_file = GTFS.get(reference_genome)
if gtf_file is None:
raise ValueError(
'get_gene_intervals requires a GTF file, or the reference genome be one of GRCh37 or GRCh38 (when on Google Cloud Platform)'
)
if gene_symbols is None and gene_ids is None and transcript_ids is None:
raise ValueError(
'get_gene_intervals requires at least one of gene_symbols, gene_ids, or transcript_ids'
)
ht = hl.experimental.import_gtf(gtf_file,
reference_genome=reference_genome,
skip_invalid_contigs=True,
min_partitions=12)
ht = ht.annotate(gene_id=ht.gene_id.split(f'\\.')[0],
transcript_id=ht.transcript_id.split('\\.')[0])
criteria = []
if gene_symbols:
criteria.append(
hl.any(lambda y: (ht.feature == 'gene') & (ht.gene_name == y),
gene_symbols))
if gene_ids:
criteria.append(
hl.any(
lambda y:
(ht.feature == 'gene') & (ht.gene_id == y.split('\\.')[0]),
gene_ids))
if transcript_ids:
criteria.append(
hl.any(
lambda y: (ht.feature == 'transcript') &
(ht.transcript_id == y.split('\\.')[0]), transcript_ids))
ht = ht.filter(functools.reduce(operator.ior, criteria))
gene_info = ht.aggregate(
hl.agg.collect((ht.feature, ht.gene_name, ht.gene_id, ht.transcript_id,
ht.interval)))
if verbose:
info(f'get_gene_intervals found {len(gene_info)} entries:\n' +
"\n".join(
map(
lambda x:
f'{x[0]}: {x[1]} ({x[2] if x[0] == "gene" else x[3]})',
gene_info)))
intervals = list(map(lambda x: x[-1], gene_info))
return intervals
def test_constructor(self):
l = Locus.parse('1:100')
self.assertEqual(l, Locus('1', 100))
self.assertEqual(l, Locus(1, 100))
self.assertEqual(l.reference_genome, hl.default_reference())
def vep_or_lookup_vep(ht,
reference_vep_ht=None,
reference=None,
vep_config_path=None,
vep_version=None):
"""
VEP a table, or lookup variants in a reference database
.. warning::
If `reference_vep_ht` is supplied, no check is performed to confirm `reference_vep_ht` was
generated with the same version of VEP / VEP configuration as the VEP referenced in `vep_config_path`.
:param ht: Input Table
:param reference_vep_ht: A reference database with VEP annotations (must be in top-level `vep`)
:param reference: If reference_vep_ht is not specified, find a suitable one in reference (if None, grabs from hl.default_reference)
:param vep_config_path: vep_config to pass to hl.vep (if None, a suitable one for `reference` is chosen)
:param vep_version: Version of VEPed context Table to use (if None, the default `vep_context` resource will be used)
:return: VEPed Table
"""
if reference is None:
reference = hl.default_reference().name
if vep_config_path is None:
vep_config_path = VEP_CONFIG_PATH
vep_help = get_vep_help(vep_config_path)
with hl.hadoop_open(vep_config_path) as vep_config_file:
vep_config = vep_config_file.read()
if reference_vep_ht is None:
if reference not in POSSIBLE_REFS:
raise ValueError(
f'vep_or_lookup_vep got {reference}. Expected one of {", ".join(POSSIBLE_REFS)}'
)
vep_context = get_vep_context(reference)
if vep_version is None:
vep_version = vep_context.default_version
if vep_version not in vep_context.versions:
logger.warning(
f"No VEPed context Table available for genome build {reference} and VEP version {vep_version}, "
f"all variants will be VEPed using the following VEP:\n{vep_help}"
)
return hl.vep(ht, vep_config_path)
logger.info(
f"Using VEPed context Table from genome build {reference} and VEP version {vep_version}"
)
reference_vep_ht = vep_context.versions[vep_version].ht()
vep_context_help = hl.eval(reference_vep_ht.vep_help)
vep_context_config = hl.eval(reference_vep_ht.vep_config)
assert vep_help == vep_context_help, (
f"The VEP context HT version does not match the version referenced in the VEP config file."
f"\nVEP context:\n{vep_context_help}\n\n VEP config:\n{vep_help}")
assert vep_config == vep_context_config, (
f"The VEP context HT configuration does not match the configuration in {vep_config_path}."
f"\nVEP context:\n{vep_context_config}\n\n Current config:\n{vep_config}"
)
ht = ht.annotate(vep=reference_vep_ht[ht.key].vep)
vep_ht = ht.filter(hl.is_defined(ht.vep))
revep_ht = ht.filter(hl.is_missing(ht.vep))
revep_ht = hl.vep(revep_ht, vep_config_path)
return vep_ht.union(revep_ht)
def get_gene_intervals(gene_symbols=None, gene_ids=None, transcript_ids=None,
verbose=True, reference_genome=None, gtf_file=None):
"""Get intervals of genes or transcripts.
Get the boundaries of genes or transcripts from a GTF file, for quick filtering of a Table or MatrixTable.
On Google Cloud platform:
Gencode v19 (GRCh37) GTF available at: gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz
Gencode v29 (GRCh38) GTF available at: gs://hail-common/references/gencode/gencode.v29.annotation.gtf.bgz
Example
-------
>>> hl.filter_intervals(ht, get_gene_intervals(gene_symbols=['PCSK9'], reference_genome='GRCh37')) # doctest: +SKIP
Parameters
----------
gene_symbols : :obj:`list` of :obj:`str`, optional
Gene symbols (e.g. PCSK9).
gene_ids : :obj:`list` of :obj:`str`, optional
Gene IDs (e.g. ENSG00000223972).
transcript_ids : :obj:`list` of :obj:`str`, optional
Transcript IDs (e.g. ENSG00000223972).
verbose : :obj:`bool`
If ``True``, print which genes and transcripts were matched in the GTF file.
reference_genome : :obj:`str` or :class:`.ReferenceGenome`, optional
Reference genome to use (passed along to import_gtf).
gtf_file : :obj:`str`
GTF file to load. If none is provided, but `reference_genome` is one of
`GRCh37` or `GRCh38`, a default will be used (on Google Cloud Platform).
Returns
-------
:obj:`list` of :class:`.Interval`
"""
GTFS = {
'GRCh37': 'gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz',
'GRCh38': 'gs://hail-common/references/gencode/gencode.v29.annotation.gtf.bgz',
}
if reference_genome is None:
reference_genome = hl.default_reference().name
if gtf_file is None:
gtf_file = GTFS.get(reference_genome)
if gtf_file is None:
raise ValueError('get_gene_intervals requires a GTF file, or the reference genome be one of GRCh37 or GRCh38 (when on Google Cloud Platform)')
if gene_symbols is None and gene_ids is None and transcript_ids is None:
raise ValueError('get_gene_intervals requires at least one of gene_symbols, gene_ids, or transcript_ids')
ht = hl.experimental.import_gtf(gtf_file, reference_genome=reference_genome,
skip_invalid_contigs=True, min_partitions=12)
ht = ht.annotate(gene_id=ht.gene_id.split(f'\\.')[0],
transcript_id=ht.transcript_id.split('\\.')[0])
criteria = []
if gene_symbols:
criteria.append(hl.any(lambda y: (ht.feature == 'gene') & (ht.gene_name == y), gene_symbols))
if gene_ids:
criteria.append(hl.any(lambda y: (ht.feature == 'gene') & (ht.gene_id == y.split('\\.')[0]), gene_ids))
if transcript_ids:
criteria.append(hl.any(lambda y: (ht.feature == 'transcript') & (ht.transcript_id == y.split('\\.')[0]), transcript_ids))
ht = ht.filter(functools.reduce(operator.ior, criteria))
gene_info = ht.aggregate(hl.agg.collect((ht.feature, ht.gene_name, ht.gene_id, ht.transcript_id, ht.interval)))
if verbose:
info(f'get_gene_intervals found {len(gene_info)} entries:\n' +
"\n".join(map(lambda x: f'{x[0]}: {x[1]} ({x[2] if x[0] == "gene" else x[3]})', gene_info)))
intervals = list(map(lambda x: x[-1], gene_info))
return intervals
def test_constructor(self):
l = Locus.parse('1:100')
self.assertEqual(l, Locus('1', 100))
self.assertEqual(l, Locus(1, 100))
self.assertEqual(l.reference_genome, hl.default_reference())
def test_classes(self):
l = Locus.parse('1:100')
self.assertEqual(l, Locus('1', 100))
self.assertEqual(l, Locus(1, 100))
self.assertEqual(l.reference_genome, hl.default_reference())
c_hom_ref = Call([0, 0])
self.assertEqual(c_hom_ref.alleles, [0, 0])
self.assertEqual(c_hom_ref.ploidy, 2)
self.assertFalse(c_hom_ref.phased)
self.assertFalse(c_hom_ref.is_haploid())
self.assertTrue(c_hom_ref.is_diploid())
self.assertEqual(c_hom_ref.n_alt_alleles(), 0)
self.assertTrue(c_hom_ref.one_hot_alleles(2) == [2, 0])
self.assertTrue(c_hom_ref.is_hom_ref())
self.assertFalse(c_hom_ref.is_het())
self.assertFalse(c_hom_ref.is_hom_var())
self.assertFalse(c_hom_ref.is_non_ref())
self.assertFalse(c_hom_ref.is_het_non_ref())
self.assertFalse(c_hom_ref.is_het_ref())
self.assertTrue(c_hom_ref.unphased_diploid_gt_index() == 0)
c_het_phased = Call([1, 0], phased=True)
self.assertEqual(c_het_phased.alleles, [1, 0])
self.assertEqual(c_het_phased.ploidy, 2)
self.assertTrue(c_het_phased.phased)
self.assertFalse(c_het_phased.is_haploid())
self.assertTrue(c_het_phased.is_diploid())
self.assertEqual(c_het_phased.n_alt_alleles(), 1)
self.assertTrue(c_het_phased.one_hot_alleles(2) == [1, 1])
self.assertFalse(c_het_phased.is_hom_ref())
self.assertTrue(c_het_phased.is_het())
self.assertFalse(c_het_phased.is_hom_var())
self.assertTrue(c_het_phased.is_non_ref())
self.assertFalse(c_het_phased.is_het_non_ref())
self.assertTrue(c_het_phased.is_het_ref())
c_hom_var = Call([1, 1])
self.assertEqual(c_hom_var.alleles, [1, 1])
self.assertEqual(c_hom_var.ploidy, 2)
self.assertFalse(c_hom_var.phased)
self.assertFalse(c_hom_var.is_haploid())
self.assertTrue(c_hom_var.is_diploid())
self.assertEqual(c_hom_var.n_alt_alleles(), 2)
self.assertTrue(c_hom_var.one_hot_alleles(2) == [0, 2])
self.assertFalse(c_hom_var.is_hom_ref())
self.assertFalse(c_hom_var.is_het())
self.assertTrue(c_hom_var.is_hom_var())
self.assertTrue(c_hom_var.is_non_ref())
self.assertFalse(c_hom_var.is_het_non_ref())
self.assertFalse(c_hom_var.is_het_ref())
self.assertTrue(c_hom_var.unphased_diploid_gt_index() == 2)
c_haploid = Call([2], phased=True)
self.assertEqual(c_haploid.alleles, [2])
self.assertEqual(c_haploid.ploidy, 1)
self.assertTrue(c_haploid.phased)
self.assertTrue(c_haploid.is_haploid())
self.assertFalse(c_haploid.is_diploid())
self.assertEqual(c_haploid.n_alt_alleles(), 1)
self.assertTrue(c_haploid.one_hot_alleles(3) == [0, 0, 1])
self.assertFalse(c_haploid.is_hom_ref())
self.assertFalse(c_haploid.is_het())
self.assertTrue(c_haploid.is_hom_var())
self.assertTrue(c_haploid.is_non_ref())
self.assertFalse(c_haploid.is_het_non_ref())
self.assertFalse(c_haploid.is_het_ref())
c_zeroploid = Call([])
self.assertEqual(c_zeroploid.alleles, [])
self.assertEqual(c_zeroploid.ploidy, 0)
self.assertFalse(c_zeroploid.phased)
self.assertFalse(c_zeroploid.is_haploid())
self.assertFalse(c_zeroploid.is_diploid())
self.assertEqual(c_zeroploid.n_alt_alleles(), 0)
self.assertTrue(c_zeroploid.one_hot_alleles(3) == [0, 0, 0])
self.assertFalse(c_zeroploid.is_hom_ref())
self.assertFalse(c_zeroploid.is_het())
self.assertFalse(c_zeroploid.is_hom_var())
self.assertFalse(c_zeroploid.is_non_ref())
self.assertFalse(c_zeroploid.is_het_non_ref())
self.assertFalse(c_zeroploid.is_het_ref())
self.assertRaisesRegex(
NotImplementedError,
"Calls with greater than 2 alleles are not supported.", Call,
[1, 1, 1, 1])
def test_classes(self):
l = Locus.parse('1:100')
self.assertEqual(l, Locus('1', 100))
self.assertEqual(l, Locus(1, 100))
self.assertEqual(l.reference_genome, hl.default_reference())
c_hom_ref = Call([0, 0])
self.assertEqual(c_hom_ref.alleles, [0, 0])
self.assertEqual(c_hom_ref.ploidy, 2)
self.assertFalse(c_hom_ref.phased)
self.assertFalse(c_hom_ref.is_haploid())
self.assertTrue(c_hom_ref.is_diploid())
self.assertEqual(c_hom_ref.n_alt_alleles(), 0)
self.assertTrue(c_hom_ref.one_hot_alleles(2) == [2, 0])
self.assertTrue(c_hom_ref.is_hom_ref())
self.assertFalse(c_hom_ref.is_het())
self.assertFalse(c_hom_ref.is_hom_var())
self.assertFalse(c_hom_ref.is_non_ref())
self.assertFalse(c_hom_ref.is_het_non_ref())
self.assertFalse(c_hom_ref.is_het_ref())
self.assertTrue(c_hom_ref.unphased_diploid_gt_index() == 0)
c_het_phased = Call([1, 0], phased=True)
self.assertEqual(c_het_phased.alleles, [1, 0])
self.assertEqual(c_het_phased.ploidy, 2)
self.assertTrue(c_het_phased.phased)
self.assertFalse(c_het_phased.is_haploid())
self.assertTrue(c_het_phased.is_diploid())
self.assertEqual(c_het_phased.n_alt_alleles(), 1)
self.assertTrue(c_het_phased.one_hot_alleles(2) == [1, 1])
self.assertFalse(c_het_phased.is_hom_ref())
self.assertTrue(c_het_phased.is_het())
self.assertFalse(c_het_phased.is_hom_var())
self.assertTrue(c_het_phased.is_non_ref())
self.assertFalse(c_het_phased.is_het_non_ref())
self.assertTrue(c_het_phased.is_het_ref())
c_hom_var = Call([1, 1])
self.assertEqual(c_hom_var.alleles, [1, 1])
self.assertEqual(c_hom_var.ploidy, 2)
self.assertFalse(c_hom_var.phased)
self.assertFalse(c_hom_var.is_haploid())
self.assertTrue(c_hom_var.is_diploid())
self.assertEqual(c_hom_var.n_alt_alleles(), 2)
self.assertTrue(c_hom_var.one_hot_alleles(2) == [0, 2])
self.assertFalse(c_hom_var.is_hom_ref())
self.assertFalse(c_hom_var.is_het())
self.assertTrue(c_hom_var.is_hom_var())
self.assertTrue(c_hom_var.is_non_ref())
self.assertFalse(c_hom_var.is_het_non_ref())
self.assertFalse(c_hom_var.is_het_ref())
self.assertTrue(c_hom_var.unphased_diploid_gt_index() == 2)
c_haploid = Call([2], phased=True)
self.assertEqual(c_haploid.alleles, [2])
self.assertEqual(c_haploid.ploidy, 1)
self.assertTrue(c_haploid.phased)
self.assertTrue(c_haploid.is_haploid())
self.assertFalse(c_haploid.is_diploid())
self.assertEqual(c_haploid.n_alt_alleles(), 1)
self.assertTrue(c_haploid.one_hot_alleles(3) == [0, 0, 1])
self.assertFalse(c_haploid.is_hom_ref())
self.assertFalse(c_haploid.is_het())
self.assertTrue(c_haploid.is_hom_var())
self.assertTrue(c_haploid.is_non_ref())
self.assertFalse(c_haploid.is_het_non_ref())
self.assertFalse(c_haploid.is_het_ref())
c_zeroploid = Call([])
self.assertEqual(c_zeroploid.alleles, [])
self.assertEqual(c_zeroploid.ploidy, 0)
self.assertFalse(c_zeroploid.phased)
self.assertFalse(c_zeroploid.is_haploid())
self.assertFalse(c_zeroploid.is_diploid())
self.assertEqual(c_zeroploid.n_alt_alleles(), 0)
self.assertTrue(c_zeroploid.one_hot_alleles(3) == [0, 0, 0])
self.assertFalse(c_zeroploid.is_hom_ref())
self.assertFalse(c_zeroploid.is_het())
self.assertFalse(c_zeroploid.is_hom_var())
self.assertFalse(c_zeroploid.is_non_ref())
self.assertFalse(c_zeroploid.is_het_non_ref())
self.assertFalse(c_zeroploid.is_het_ref())
self.assertRaisesRegex(
NotImplementedError,
"Calls with greater than 2 alleles are not supported.", Call,
[1, 1, 1, 1])
rg = hl.get_reference('GRCh37')
self.assertEqual(rg.name, "GRCh37")
self.assertEqual(rg.contigs[0], "1")
self.assertListEqual(rg.x_contigs, ["X"])
self.assertListEqual(rg.y_contigs, ["Y"])
self.assertListEqual(rg.mt_contigs, ["MT"])
self.assertEqual(rg.par[0],
hl.parse_locus_interval("X:60001-2699521").value)
self.assertEqual(rg.contig_length("1"), 249250621)
name = "test"
contigs = ["1", "X", "Y", "MT"]
lengths = {"1": 10000, "X": 2000, "Y": 4000, "MT": 1000}
x_contigs = ["X"]
y_contigs = ["Y"]
mt_contigs = ["MT"]
par = [("X", 5, 1000)]
gr2 = ReferenceGenome(name, contigs, lengths, x_contigs, y_contigs,
mt_contigs, par)
self.assertEqual(gr2.name, name)
self.assertListEqual(gr2.contigs, contigs)
self.assertListEqual(gr2.x_contigs, x_contigs)
self.assertListEqual(gr2.y_contigs, y_contigs)
self.assertListEqual(gr2.mt_contigs, mt_contigs)
self.assertEqual(gr2.par,
[hl.parse_locus_interval("X:5-1000", gr2).value])
self.assertEqual(gr2.contig_length("1"), 10000)
self.assertDictEqual(gr2.lengths, lengths)
gr2.write("/tmp/my_gr.json")
gr3 = ReferenceGenome.read(resource("fake_ref_genome.json"))
self.assertEqual(gr3.name, "my_reference_genome")
self.assertFalse(gr3.has_sequence())
gr4 = ReferenceGenome.from_fasta_file(
"test_rg",
resource("fake_reference.fasta"),
resource("fake_reference.fasta.fai"),
mt_contigs=["b", "c"],
x_contigs=["a"])
self.assertTrue(gr4.has_sequence())
self.assertTrue(gr4.x_contigs == ["a"])
t = hl.import_table(resource("fake_reference.tsv"), impute=True)
self.assertTrue(t.all(hl.get_sequence(gr4, t.contig, t.pos) == t.base))
l = hl.locus("a", 7, gr4)
self.assertTrue(
l.sequence_context(before=3, after=3).value == "TTTCGAA")
