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test_impex.py
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test_impex.py
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import json
import os
import pytest
import shutil
import unittest
from unittest import mock
from avro.datafile import DataFileReader
from avro.io import DatumReader
from hail.context import TemporaryFilename
import pytest
import hail as hl
from ..helpers import *
from hail import ir
from hail.utils import new_temp_file, new_local_temp_file, FatalError, run_command, uri_path, HailUserError
_FLOAT_INFO_FIELDS = [
'BaseQRankSum',
'ClippingRankSum',
'FS',
'GQ_MEAN',
'GQ_STDDEV',
'HWP',
'HaplotypeScore',
'InbreedingCoeff',
'MQ',
'MQRankSum',
'QD',
'ReadPosRankSum',
'VQSLOD',
]
_FLOAT_ARRAY_INFO_FIELDS = ['AF', 'MLEAF']
def _vcf_unsorted_alleles():
mt = hl.import_vcf(resource('sample.pksorted.vcf'), n_partitions=4)
mt.rows()._force_count()
class VCFTests(unittest.TestCase):
def test_info_char(self):
self.assertEqual(hl.import_vcf(resource('infochar.vcf')).count_rows(), 1)
def test_info_float64(self):
"""Test that floating-point info fields are 64-bit regardless of the entry float type"""
mt = hl.import_vcf(resource('infochar.vcf'), entry_float_type=hl.tfloat32)
for f in _FLOAT_INFO_FIELDS:
self.assertEqual(mt['info'][f].dtype, hl.tfloat64)
for f in _FLOAT_ARRAY_INFO_FIELDS:
self.assertEqual(mt['info'][f].dtype, hl.tarray(hl.tfloat64))
@qobtest
def test_glob(self):
full = hl.import_vcf(resource('sample.vcf'))
parts = hl.import_vcf(resource('samplepart*.vcf'))
self.assertTrue(parts._same(full))
def test_undeclared_info(self):
mt = hl.import_vcf(resource('undeclaredinfo.vcf'))
rows = mt.rows()
self.assertTrue(rows.all(hl.is_defined(rows.info)))
info_type = mt.row.dtype['info']
self.assertTrue('InbreedingCoeff' in info_type)
self.assertFalse('undeclared' in info_type)
self.assertFalse('undeclaredFlag' in info_type)
def test_can_import_bad_number_flag(self):
hl.import_vcf(resource('bad_flag_number.vcf')).rows()._force_count()
def test_malformed(self):
with self.assertRaisesRegex(FatalError, "invalid character"):
mt = hl.import_vcf(resource('malformed.vcf'))
mt._force_count_rows()
def test_not_identical_headers(self):
t = new_temp_file(extension='vcf')
mt = hl.import_vcf(resource('sample.vcf'))
hl.export_vcf(mt.filter_cols((mt.s != "C1048::HG02024") & (mt.s != "HG00255")), t)
with self.assertRaisesRegex(FatalError, 'invalid sample IDs'):
(hl.import_vcf([resource('sample.vcf'), t])._force_count_rows())
def test_filter(self):
mt = hl.import_vcf(resource('malformed.vcf'), filter='rs685723')
mt._force_count_rows()
mt = hl.import_vcf(resource('sample.vcf'), filter=r'\trs\d+\t')
assert mt.aggregate_rows(hl.agg.all(hl.is_missing(mt.rsid)))
def test_find_replace(self):
mt = hl.import_vcf(resource('sample.vcf'), find_replace=(r'\trs\d+\t', '\t.\t'))
mt.rows().show()
assert mt.aggregate_rows(hl.agg.all(hl.is_missing(mt.rsid)))
def test_haploid(self):
expected = hl.Table.parallelize(
[
hl.struct(locus=hl.locus("X", 16050036), s="C1046::HG02024", GT=hl.call(0, 0), AD=[10, 0], GQ=44),
hl.struct(locus=hl.locus("X", 16050036), s="C1046::HG02025", GT=hl.call(1), AD=[0, 6], GQ=70),
hl.struct(locus=hl.locus("X", 16061250), s="C1046::HG02024", GT=hl.call(2, 2), AD=[0, 0, 11], GQ=33),
hl.struct(locus=hl.locus("X", 16061250), s="C1046::HG02025", GT=hl.call(2), AD=[0, 0, 9], GQ=24),
],
key=['locus', 's'],
)
mt = hl.import_vcf(resource('haploid.vcf'))
entries = mt.entries()
entries = entries.key_by('locus', 's')
entries = entries.select('GT', 'AD', 'GQ')
self.assertTrue(entries._same(expected))
def test_call_fields(self):
expected = hl.Table.parallelize(
[
hl.struct(
locus=hl.locus("X", 16050036),
s="C1046::HG02024",
GT=hl.call(0, 0),
GTA=hl.missing(hl.tcall),
GTZ=hl.call(0, 1),
),
hl.struct(
locus=hl.locus("X", 16050036),
s="C1046::HG02025",
GT=hl.call(1),
GTA=hl.missing(hl.tcall),
GTZ=hl.call(0),
),
hl.struct(
locus=hl.locus("X", 16061250),
s="C1046::HG02024",
GT=hl.call(2, 2),
GTA=hl.call(2, 1),
GTZ=hl.call(1, 1),
),
hl.struct(
locus=hl.locus("X", 16061250),
s="C1046::HG02025",
GT=hl.call(2),
GTA=hl.missing(hl.tcall),
GTZ=hl.call(1),
),
],
key=['locus', 's'],
)
mt = hl.import_vcf(resource('generic.vcf'), call_fields=['GT', 'GTA', 'GTZ'])
entries = mt.entries()
entries = entries.key_by('locus', 's')
entries = entries.select('GT', 'GTA', 'GTZ')
self.assertTrue(entries._same(expected))
def test_import_vcf(self):
vcf = hl.split_multi_hts(
hl.import_vcf(
resource('sample2.vcf'), reference_genome=hl.get_reference('GRCh38'), contig_recoding={"22": "chr22"}
)
)
vcf_table = vcf.rows()
self.assertTrue(vcf_table.all(vcf_table.locus.contig == "chr22"))
self.assertTrue(vcf.locus.dtype, hl.tlocus('GRCh37'))
def test_import_vcf_empty(self):
mt = hl.import_vcf([resource('0var.vcf.bgz'), resource('3var.vcf.bgz')])
assert mt._same(hl.import_vcf(resource('3var.vcf.bgz')))
def test_import_vcf_no_reference_specified(self):
vcf = hl.import_vcf(resource('sample2.vcf'), reference_genome=None)
self.assertEqual(vcf.locus.dtype, hl.tstruct(contig=hl.tstr, position=hl.tint32))
self.assertEqual(vcf.count_rows(), 735)
def test_import_vcf_bad_reference_allele(self):
vcf = hl.import_vcf(resource('invalid_base.vcf'))
self.assertEqual(vcf.count_rows(), 1)
def test_import_vcf_flags_are_defined(self):
# issue 3277
t = hl.import_vcf(resource('sample.vcf')).rows()
self.assertTrue(
t.all(
hl.is_defined(t.info.NEGATIVE_TRAIN_SITE)
& hl.is_defined(t.info.POSITIVE_TRAIN_SITE)
& hl.is_defined(t.info.DB)
& hl.is_defined(t.info.DS)
)
)
def test_import_vcf_can_import_float_array_format(self):
mt = hl.import_vcf(resource('floating_point_array.vcf'))
self.assertTrue(mt.aggregate_entries(hl.agg.all(mt.numeric_array == [1.5, 2.5])))
self.assertEqual(hl.tarray(hl.tfloat64), mt['numeric_array'].dtype)
def test_import_vcf_can_import_float32_array_format(self):
mt = hl.import_vcf(resource('floating_point_array.vcf'), entry_float_type=hl.tfloat32)
self.assertTrue(mt.aggregate_entries(hl.agg.all(mt.numeric_array == [1.5, 2.5])))
self.assertEqual(hl.tarray(hl.tfloat32), mt['numeric_array'].dtype)
def test_import_vcf_can_import_negative_numbers(self):
mt = hl.import_vcf(resource('negative_format_fields.vcf'))
self.assertTrue(
mt.aggregate_entries(
hl.agg.all(mt.negative_int == -1)
& hl.agg.all(mt.negative_float == -1.5)
& hl.agg.all(mt.negative_int_array == [-1, -2])
& hl.agg.all(mt.negative_float_array == [-0.5, -1.5])
)
)
def test_import_vcf_has_good_error_message_when_info_fields_have_missing_elements(self):
mt = hl.import_vcf(resource('missingInfoArray.vcf'), reference_genome='GRCh37')
with pytest.raises(
FatalError,
match=".*Missing value in INFO array. Use 'hl.import_vcf[(][.][.][.], array_elements_required=False[)]'[.].*",
):
mt._force_count_rows()
def test_import_vcf_array_elements_required_is_false_parses_info_fields_with_missing_elements(self):
mt = hl.import_vcf(resource('missingInfoArray.vcf'), reference_genome='GRCh37', array_elements_required=False)
mt = mt.select_rows(**mt.info)
expected = hl.Table.parallelize(
[
{
'locus': hl.Locus('X', 16050036),
'alleles': ['A', 'C'],
'FOO': [1, None],
'BAR': [2, None, None],
'JUST_A_DOT': None,
'NOT_EVEN_PRESENT': None,
},
{
'locus': hl.Locus('X', 16061250),
'alleles': ['T', 'A', 'C'],
'FOO': [None, 2, None],
'BAR': [None, 1.0, None],
'JUST_A_DOT': None,
'NOT_EVEN_PRESENT': None,
},
],
hl.tstruct(
locus=hl.tlocus('GRCh37'),
alleles=hl.tarray(hl.tstr),
FOO=hl.tarray(hl.tint),
BAR=hl.tarray(hl.tfloat64),
JUST_A_DOT=hl.tarray(hl.tfloat64),
NOT_EVEN_PRESENT=hl.tarray(hl.tfloat64),
),
key=['locus', 'alleles'],
)
assert mt.rows()._same(expected)
def test_import_vcf_missing_format_field_elements(self):
mt = hl.import_vcf(resource('missingFormatArray.vcf'), reference_genome='GRCh37', array_elements_required=False)
mt = mt.select_rows().select_entries('AD', 'PL')
expected = hl.Table.parallelize(
[
{
'locus': hl.Locus('X', 16050036),
'alleles': ['A', 'C'],
's': 'C1046::HG02024',
'AD': [None, None],
'PL': [0, None, 180],
},
{
'locus': hl.Locus('X', 16050036),
'alleles': ['A', 'C'],
's': 'C1046::HG02025',
'AD': [None, 6],
'PL': [70, None],
},
{
'locus': hl.Locus('X', 16061250),
'alleles': ['T', 'A', 'C'],
's': 'C1046::HG02024',
'AD': [0, 0, None],
'PL': [396, None, None, 33, None, 0],
},
{
'locus': hl.Locus('X', 16061250),
'alleles': ['T', 'A', 'C'],
's': 'C1046::HG02025',
'AD': [0, 0, 9],
'PL': [None, None, None],
},
],
hl.tstruct(
locus=hl.tlocus('GRCh37'),
alleles=hl.tarray(hl.tstr),
s=hl.tstr,
AD=hl.tarray(hl.tint),
PL=hl.tarray(hl.tint),
),
key=['locus', 'alleles', 's'],
)
self.assertTrue(mt.entries()._same(expected))
def test_vcf_unsorted_alleles(self):
_vcf_unsorted_alleles()
def test_vcf_unsorted_alleles_no_codegen(self):
with_flags(no_whole_stage_codegen="1")(_vcf_unsorted_alleles)()
def test_import_vcf_skip_invalid_loci(self):
mt = hl.import_vcf(resource('skip_invalid_loci.vcf'), reference_genome='GRCh37', skip_invalid_loci=True)
self.assertEqual(mt._force_count_rows(), 3)
with self.assertRaisesRegex(FatalError, 'Invalid locus'):
hl.import_vcf(resource('skip_invalid_loci.vcf')).count()
def test_import_vcf_set_field_missing(self):
mt = hl.import_vcf(resource('test_set_field_missing.vcf'))
mt.aggregate_entries(hl.agg.sum(mt.DP))
def test_import_vcf_dosages_as_doubles_or_floats(self):
mt = hl.import_vcf(resource('small-ds.vcf'))
self.assertEqual(hl.expr.expressions.typed_expressions.Float64Expression, type(mt.entry.DS))
mt32 = hl.import_vcf(resource('small-ds.vcf'), entry_float_type=hl.tfloat32)
self.assertEqual(hl.expr.expressions.typed_expressions.Float32Expression, type(mt32.entry.DS))
mt_result = mt.annotate_entries(DS32=mt32.index_entries(mt.row_key, mt.col_key).DS)
compare = mt_result.annotate_entries(
test=(hl.coalesce(hl.approx_equal(mt_result.DS, mt_result.DS32, nan_same=True), True))
)
self.assertTrue(all(compare.test.collect()))
def test_import_vcf_invalid_float_type(self):
with self.assertRaises(TypeError):
mt = hl.import_vcf(resource('small-ds.vcf'), entry_float_type=hl.tstr)
with self.assertRaises(TypeError):
mt = hl.import_vcf(resource('small-ds.vcf'), entry_float_type=hl.tint)
with self.assertRaises(TypeError):
mt = hl.import_vcf(resource('small-ds.vcf'), entry_float_type=hl.tint32)
with self.assertRaises(TypeError):
mt = hl.import_vcf(resource('small-ds.vcf'), entry_float_type=hl.tint64)
def test_export_vcf(self):
dataset = hl.import_vcf(resource('sample.vcf.bgz'))
vcf_metadata = hl.get_vcf_metadata(resource('sample.vcf.bgz'))
with TemporaryFilename(suffix='.vcf') as sample_vcf, TemporaryFilename(suffix='.vcf') as no_sample_vcf:
hl.export_vcf(dataset, sample_vcf, metadata=vcf_metadata)
dataset_imported = hl.import_vcf(sample_vcf)
self.assertTrue(dataset._same(dataset_imported))
no_sample_dataset = dataset.filter_cols(False).select_entries()
hl.export_vcf(no_sample_dataset, no_sample_vcf, metadata=vcf_metadata)
no_sample_dataset_imported = hl.import_vcf(no_sample_vcf)
self.assertTrue(no_sample_dataset._same(no_sample_dataset_imported))
metadata_imported = hl.get_vcf_metadata(sample_vcf)
# are py4 JavaMaps, not dicts, so can't use assertDictEqual
self.assertEqual(vcf_metadata, metadata_imported)
def test_export_vcf_quotes_and_backslash_in_description(self):
ds = hl.import_vcf(resource("sample.vcf"))
meta = hl.get_vcf_metadata(resource("sample.vcf"))
meta["info"]["AF"]["Description"] = 'foo "bar" \\'
with TemporaryFilename(suffix='.vcf') as test_vcf:
hl.export_vcf(ds, test_vcf, metadata=meta)
af_lines = [
line
for line in hl.current_backend().fs.open(test_vcf).read().split('\n')
if line.startswith("##INFO=<ID=AF")
]
assert len(af_lines) == 1, af_lines
line = af_lines[0]
assert line.startswith("##INFO=<") and line.endswith(">"), line
line = line[8:-1]
fields = dict([f.split("=") for f in line.split(",")])
description = fields["Description"]
assert description == '"foo \\"bar\\" \\\\"'
def test_export_vcf_empty_format(self):
mt = hl.import_vcf(resource('sample.vcf.bgz')).select_entries()
tmp = new_temp_file(extension="vcf")
hl.export_vcf(mt, tmp)
assert hl.import_vcf(tmp)._same(mt)
def test_export_vcf_no_gt(self):
mt = hl.import_vcf(resource('sample.vcf.bgz')).drop('GT')
tmp = new_temp_file(extension="vcf")
hl.export_vcf(mt, tmp)
assert hl.import_vcf(tmp)._same(mt)
def test_export_vcf_no_alt_alleles(self):
mt = hl.import_vcf(resource('gvcfs/HG0096_excerpt.g.vcf'), reference_genome='GRCh38')
self.assertEqual(mt.filter_rows(hl.len(mt.alleles) == 1).count_rows(), 5)
tmp = new_temp_file(extension="vcf")
hl.export_vcf(mt, tmp)
mt2 = hl.import_vcf(tmp, reference_genome='GRCh38')
self.assertTrue(mt._same(mt2))
def test_export_sites_only_from_table(self):
mt = hl.import_vcf(resource('sample.vcf.bgz')).select_entries().filter_cols(False)
tmp = new_temp_file(extension="vcf")
hl.export_vcf(mt.rows(), tmp)
assert hl.import_vcf(tmp)._same(mt)
def test_export_vcf_invalid_info_types(self):
ds = hl.import_vcf(resource("sample.vcf"))
ds = ds.annotate_rows(
info=ds.info.annotate(
arr_bool=hl.missing(hl.tarray(hl.tbool)), arr_arr_i32=hl.missing(hl.tarray(hl.tarray(hl.tint32)))
)
)
with pytest.raises(FatalError) as exp, TemporaryFilename(suffix='.vcf') as export_path:
hl.export_vcf(ds, export_path)
msg = '''VCF does not support the type(s) for the following INFO field(s):
\t'arr_bool': 'array<bool>'.
\t'arr_arr_i32': 'array<array<int32>>'.
'''
assert msg in str(exp.value)
def test_export_vcf_invalid_format_types(self):
ds = hl.import_vcf(resource("sample.vcf"))
ds = ds.annotate_entries(boolean=hl.missing(hl.tbool), arr_arr_i32=hl.missing(hl.tarray(hl.tarray(hl.tint32))))
with pytest.raises(FatalError) as exp, TemporaryFilename(suffix='.vcf') as export_path:
hl.export_vcf(ds, export_path)
msg = '''VCF does not support the type(s) for the following FORMAT field(s):
\t'boolean': 'bool'.
\t'arr_arr_i32': 'array<array<int32>>'.
'''
assert msg in str(exp.value)
def import_gvcfs_sample_vcf(self, path):
parts_type = hl.tarray(hl.tinterval(hl.tstruct(locus=hl.tlocus('GRCh37'))))
parts = [
hl.Interval(
start=hl.Struct(locus=hl.Locus('20', 1)),
end=hl.Struct(locus=hl.Locus('20', 13509135)),
includes_end=True,
),
hl.Interval(
start=hl.Struct(locus=hl.Locus('20', 13509136)),
end=hl.Struct(locus=hl.Locus('20', 16493533)),
includes_end=True,
),
hl.Interval(
start=hl.Struct(locus=hl.Locus('20', 16493534)),
end=hl.Struct(locus=hl.Locus('20', 20000000)),
includes_end=True,
),
]
parts_str = json.dumps(parts_type._convert_to_json(parts))
vir = ir.MatrixVCFReader(
path=path,
call_fields=['PGT'],
entry_float_type=hl.tfloat64,
header_file=None,
block_size=None,
min_partitions=None,
reference_genome='default',
contig_recoding=None,
array_elements_required=True,
skip_invalid_loci=False,
force_bgz=False,
force_gz=False,
filter=None,
find_replace=None,
n_partitions=None,
_partitions_json=parts_str,
_partitions_type=parts_type,
)
vcf1 = hl.import_vcf(path)
vcf2 = hl.MatrixTable(ir.MatrixRead(vir))
self.assertEqual(len(parts), vcf2.n_partitions())
self.assertTrue(vcf1._same(vcf2))
interval = [hl.parse_locus_interval('[20:13509136-16493533]')]
filter1 = hl.filter_intervals(vcf1, interval)
filter2 = hl.filter_intervals(vcf2, interval)
self.assertEqual(1, filter2.n_partitions())
self.assertTrue(filter1._same(filter2))
# we've selected exactly the middle partition ±1 position on either end
interval_a = [hl.parse_locus_interval('[20:13509135-16493533]')]
interval_b = [hl.parse_locus_interval('[20:13509136-16493534]')]
interval_c = [hl.parse_locus_interval('[20:13509135-16493534]')]
self.assertEqual(hl.filter_intervals(vcf2, interval_a).n_partitions(), 2)
self.assertEqual(hl.filter_intervals(vcf2, interval_b).n_partitions(), 2)
self.assertEqual(hl.filter_intervals(vcf2, interval_c).n_partitions(), 3)
def test_tabix_export(self):
mt = hl.import_vcf(resource('sample.vcf.bgz'))
tmp = new_temp_file(extension="bgz")
hl.export_vcf(mt, tmp, tabix=True)
self.import_gvcfs_sample_vcf(tmp)
def test_tabix_export_file_exists(self):
mt = hl.import_vcf(resource('sample.vcf.bgz'))
tmp = new_temp_file(extension="bgz")
hl.export_vcf(mt, tmp, tabix=True, parallel='header_per_shard')
files = hl.current_backend().fs.ls(tmp)
self.assertTrue(any(f.path.endswith('.tbi') for f in files))
@qobtest
def test_import_gvcfs(self):
path = resource('sample.vcf.bgz')
self.import_gvcfs_sample_vcf(path)
def test_import_gvcfs_long_line(self):
import bz2
fs = hl.current_backend().fs
path = resource('gvcfs/long_line.g.vcf.gz')
vcf = hl.import_vcf(path, force_bgz=True)
[data] = vcf.info.Custom.collect()
with fs.open(resource('gvcfs/long_line.ref.bz2'), 'rb') as ref:
ref_str = bz2.open(ref).read().decode('utf-8')
self.assertEqual(ref_str, data)
def test_vcf_parser_golden_master__ex_GRCh37(self):
self._test_vcf_parser_golden_master(resource('ex.vcf'), 'GRCh37')
def test_vcf_parser_golden_master__sample_GRCh37(self):
self._test_vcf_parser_golden_master(resource('sample.vcf'), 'GRCh37')
@test_timeout(6 * 60)
def test_vcf_parser_golden_master__gvcf_GRCh37(self):
self._test_vcf_parser_golden_master(resource('gvcfs/HG00096.g.vcf.gz'), 'GRCh38')
def _test_vcf_parser_golden_master(self, vcf_path, rg):
vcf = hl.import_vcf(vcf_path, reference_genome=rg, array_elements_required=False, force_bgz=True)
mt = hl.read_matrix_table(vcf_path + '.mt')
self.assertTrue(mt._same(vcf))
def test_combiner_works(self):
from hail.vds.combiner.combine import transform_gvcf, combine_variant_datasets
_paths = ['gvcfs/HG00096.g.vcf.gz', 'gvcfs/HG00268.g.vcf.gz']
paths = [resource(p) for p in _paths]
vdses = []
for path in paths:
mt = hl.import_vcf(path, reference_genome='GRCh38', array_elements_required=False, force_bgz=True)
mt = transform_gvcf(
mt.annotate_rows(
info=mt.info.annotate(
MQ_DP=hl.missing(hl.tint32), VarDP=hl.missing(hl.tint32), QUALapprox=hl.missing(hl.tint32)
)
),
reference_entry_fields_to_keep=[],
)
vdses.append(mt)
comb = combine_variant_datasets(vdses)
assert comb.reference_data._force_count_rows() == 458646
assert comb.variant_data._force_count_rows() == 14346
def test_haploid_combiner_ok(self):
from hail.vds.combiner.combine import transform_gvcf
# make a combiner table
mt = hl.utils.range_matrix_table(2, 1)
mt = mt.annotate_cols(s='S01')
mt = mt.key_cols_by('s')
mt = mt.select_cols()
mt = mt.annotate_rows(locus=hl.locus(contig='chrX', pos=mt.row_idx + 100, reference_genome='GRCh38'))
mt = mt.key_rows_by('locus')
mt = mt.annotate_rows(alleles=['A', '<NON_REF>'])
mt = mt.annotate_entries(GT=hl.if_else((mt.row_idx % 2) == 0, hl.call(0), hl.call(0, 0)))
mt = mt.annotate_entries(DP=31)
mt = mt.annotate_entries(GQ=30)
mt = mt.annotate_entries(PL=hl.if_else((mt.row_idx % 2) == 0, [0, 20], [0, 20, 400]))
mt = mt.annotate_rows(info=hl.struct(END=mt.locus.position))
mt = mt.annotate_rows(rsid=hl.missing(hl.tstr))
mt = mt.drop('row_idx')
vds = transform_gvcf(mt, [])
vds.reference_data._force_count_rows()
vds.variant_data._force_count_rows()
def test_combiner_parse_allele_specific_annotations(self):
from hail.vds.combiner.combine import parse_allele_specific_fields
infos = hl.array(
[
hl.struct(
AS_QUALapprox="|1171|",
AS_SB_TABLE="0,0|30,27|0,0",
AS_VarDP="0|57|0",
AS_RAW_MQ="0.00|15100.00|0.00",
AS_RAW_MQRankSum="|0.0,1|NaN",
AS_RAW_ReadPosRankSum="|0.7,1|NaN",
),
hl.struct(
AS_QUALapprox="|1171|",
AS_SB_TABLE="0,0|30,27|0,0",
AS_VarDP="0|57|0",
AS_RAW_MQ="0.00|15100.00|0.00",
AS_RAW_MQRankSum="|NaN|NaN",
AS_RAW_ReadPosRankSum="|NaN|NaN",
),
]
)
output = hl.eval(infos.map(lambda info: parse_allele_specific_fields(info, False)))
expected = [
hl.Struct(
AS_QUALapprox=[None, 1171, None],
AS_SB_TABLE=[[0, 0], [30, 27], [0, 0]],
AS_VarDP=[0, 57, 0],
AS_RAW_MQ=[0.00, 15100.00, 0.00],
AS_RAW_MQRankSum=[None, (0.0, 1), None],
AS_RAW_ReadPosRankSum=[None, (0.7, 1), None],
),
hl.Struct(
AS_QUALapprox=[None, 1171, None],
AS_SB_TABLE=[[0, 0], [30, 27], [0, 0]],
AS_VarDP=[0, 57, 0],
AS_RAW_MQ=[0.00, 15100.00, 0.00],
AS_RAW_MQRankSum=[None, None, None],
AS_RAW_ReadPosRankSum=[None, None, None],
),
]
assert output == expected
def test_flag_at_eol(self):
vcf_path = resource('flag_at_end.vcf')
mt = hl.import_vcf(vcf_path)
assert mt._force_count_rows() == 1
def test_missing_float_entries(self):
vcf = hl.import_vcf(resource('noglgp.vcf'), array_elements_required=False, reference_genome='GRCh38')
gl_gp = vcf.aggregate_entries(hl.agg.collect(hl.struct(GL=vcf.GL, GP=vcf.GP)))
assert gl_gp == [
hl.Struct(GL=[None, None, None], GP=[0.22, 0.5, 0.27]),
hl.Struct(GL=[None, None, None], GP=[None, None, None]),
]
def test_same_bgzip(self):
mt = hl.import_vcf(resource('sample.vcf'), min_partitions=4)
f = new_temp_file(extension='vcf.bgz')
hl.export_vcf(mt, f)
assert hl.import_vcf(f)._same(mt)
def test_vcf_parallel_separate_header_export(self):
fs = hl.current_backend().fs
def concat_files(outpath, inpaths):
with fs.open(outpath, 'wb') as outfile:
for path in inpaths:
with fs.open(path, 'rb') as infile:
shutil.copyfileobj(infile, outfile)
mt = hl.import_vcf(resource('sample.vcf'), min_partitions=4)
f = new_temp_file(extension='vcf.bgz')
hl.export_vcf(mt, f, parallel='separate_header')
stat = fs.stat(f)
assert stat
assert stat.is_dir()
shard_paths = [info.path for info in fs.ls(f) if os.path.splitext(info.path)[-1] == '.bgz']
assert shard_paths
shard_paths.sort()
nf = new_temp_file(extension='vcf.bgz')
concat_files(nf, shard_paths)
assert hl.import_vcf(nf)._same(mt)
manifest_files = [os.path.join(f, line.strip()) for line in fs.open(os.path.join(f, 'shard-manifest.txt'))]
assert hl.import_vcf(manifest_files[1:], header_file=manifest_files[0])._same(mt)
assert [p.split('/')[-1] for p in shard_paths] == [p.split('/')[-1] for p in manifest_files]
def test_custom_rg_import(self):
rg = hl.ReferenceGenome.read(resource('deid_ref_genome.json'))
mt = hl.import_vcf(resource('custom_rg.vcf'), reference_genome=rg)
assert mt.locus.collect() == [hl.Locus('D', 123, reference_genome=rg)]
def test_sorted(self):
mt = hl.utils.range_matrix_table(10, 10, n_partitions=4).filter_cols(False)
mt = mt.key_cols_by(s='dummy')
mt = mt.annotate_entries(GT=hl.unphased_diploid_gt_index_call(0))
mt = mt.key_rows_by(locus=hl.locus('1', 100 - mt.row_idx), alleles=['A', 'T'])
f = new_temp_file(extension='vcf')
hl.export_vcf(mt, f)
last = 0
with hl.current_backend().fs.open(f, 'r') as i:
for line in i:
if line.startswith('#'):
continue
else:
pos = int(line.split('\t')[1])
assert pos >= last
last = pos
def test_empty_read_write(self):
mt = hl.import_vcf(resource('sample.vcf'), min_partitions=4).filter_rows(False)
out1 = new_temp_file(extension='vcf')
out2 = new_temp_file(extension='vcf.bgz')
hl.export_vcf(mt, out1)
hl.export_vcf(mt, out2)
assert hl.current_backend().fs.stat(out1).size > 0
assert hl.current_backend().fs.stat(out2).size > 0
assert hl.import_vcf(out1)._same(mt)
assert hl.import_vcf(out2)._same(mt)
def test_empty_import_vcf_group_by_collect(self):
mt = hl.import_vcf(resource('sample.vcf'), min_partitions=4).filter_rows(False)
ht = mt._localize_entries('entries', 'columns')
groups = ht.group_by(the_key=ht.key).aggregate(values=hl.agg.collect(ht.row_value)).collect()
assert not groups
def test_format_header(self):
mt = hl.import_vcf(resource('sample2.vcf'))
metadata = hl.get_vcf_metadata(resource('sample2.vcf'))
f = new_temp_file(extension='vcf')
hl.export_vcf(mt, f, metadata=metadata)
s = set()
with hl.current_backend().fs.open(f, 'r') as i:
for line in i:
if line.startswith('##FORMAT'):
s.add(line.strip())
assert s == {
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">',
'##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">',
'##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">',
'##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">',
}
def test_format_genotypes(self):
mt = hl.import_vcf(resource('sample.vcf'))
f = new_temp_file(extension='vcf')
hl.export_vcf(mt, f)
with hl.current_backend().fs.open(f, 'r') as i:
for line in i:
if line.startswith('20\t13029920'):
expected = (
"GT:AD:DP:GQ:PL\t1/1:0,6:6:18:234,18,0\t1/1:0,4:4:12:159,12,0\t"
"1/1:0,4:4:12:163,12,0\t1/1:0,12:12:36:479,36,0\t"
"1/1:0,4:4:12:149,12,0\t1/1:0,6:6:18:232,18,0\t"
"1/1:0,6:6:18:242,18,0\t1/1:0,3:3:9:119,9,0\t1/1:0,9:9:27:374,27,0"
"\t./.:1,0:1\t1/1:0,3:3:9:133,9,0"
)
assert expected in line
break
else:
assert False, 'expected pattern not found'
def test_contigs_header(self):
mt = hl.import_vcf(resource('sample.vcf')).filter_cols(False)
f = new_temp_file(extension='vcf')
hl.export_vcf(mt, f)
with hl.current_backend().fs.open(f, 'r') as i:
for line in i:
if line.startswith('##contig=<ID=10'):
assert line.strip() == '##contig=<ID=10,length=135534747,assembly=GRCh37>'
break
else:
assert False, 'expected pattern not found'
def test_metadata_argument(self):
mt = hl.import_vcf(resource('multipleChromosomes.vcf'))
f = new_temp_file(extension='vcf')
metadata = {
'filter': {'LowQual': {'Description': 'Low quality'}},
'format': {'GT': {'Description': 'Genotype call.', 'Number': 'foo'}},
'fakeField': {},
}
hl.export_vcf(mt, f, metadata=metadata)
saw_gt = False
saw_lq = False
with hl.current_backend().fs.open(f, 'r') as f:
for line in f:
print(line[:25])
if line.startswith('##FORMAT=<ID=GT'):
assert line.strip() == '##FORMAT=<ID=GT,Number=foo,Type=String,Description="Genotype call.">'
assert not saw_gt
saw_gt = True
elif line.startswith('##FILTER=<ID=LowQual'):
assert line.strip() == '##FILTER=<ID=LowQual,Description="Low quality">'
assert not saw_lq
saw_lq = True
assert saw_gt
assert saw_lq
def test_invalid_info_fields(self):
t = new_temp_file(extension='vcf')
mt = hl.import_vcf(resource('sample.vcf'))
with mock.patch("hail.methods.impex.warning", autospec=True) as warning:
hl.export_vcf(mt, t)
assert warning.call_count == 0
for invalid_field in ["foo-1", "123", "bar baz"]:
with mock.patch("hail.methods.impex.warning", autospec=True) as warning:
hl.export_vcf(mt.annotate_rows(info=mt.info.annotate(**{invalid_field: True})), t)
assert warning.call_count == 1
def test_vcf_different_info_errors(self):
with self.assertRaisesRegex(FatalError, "Check that all files have same INFO fields"):
mt = hl.import_vcf([resource('different_info_test1.vcf'), resource('different_info_test2.vcf')])
mt.rows()._force_count()
class PLINKTests(unittest.TestCase):
def test_import_fam(self):
fam_file = resource('sample.fam')
nfam = hl.import_fam(fam_file).count()
i = 0
with hl.current_backend().fs.open(fam_file) as f:
for line in f:
if len(line.strip()) != 0:
i += 1
self.assertEqual(nfam, i)
def test_export_import_plink_same(self):
mt = get_dataset()
mt = mt.select_rows(
rsid=hl.delimit([mt.locus.contig, hl.str(mt.locus.position), mt.alleles[0], mt.alleles[1]], ':'),
cm_position=15.0,
)
mt = mt.select_cols(
fam_id=hl.missing(hl.tstr),
pat_id=hl.missing(hl.tstr),
mat_id=hl.missing(hl.tstr),
is_female=hl.missing(hl.tbool),
is_case=hl.missing(hl.tbool),
)
mt = mt.select_entries('GT')
bfile = new_temp_file(prefix='test_import_export_plink')
hl.export_plink(mt, bfile, ind_id=mt.s, cm_position=mt.cm_position)
mt_imported = hl.import_plink(
bfile + '.bed', bfile + '.bim', bfile + '.fam', a2_reference=True, reference_genome='GRCh37', n_partitions=8
)
self.assertTrue(mt._same(mt_imported))
self.assertTrue(mt.aggregate_rows(hl.agg.all(mt.cm_position == 15.0)))
def test_import_plink_empty_fam(self):
mt = get_dataset().filter_cols(False)
bfile = new_temp_file(prefix='test_empty_fam')
hl.export_plink(mt, bfile, ind_id=mt.s)
with self.assertRaisesRegex(FatalError, "Empty FAM file"):
hl.import_plink(bfile + '.bed', bfile + '.bim', bfile + '.fam')
def test_import_plink_empty_bim(self):
mt = get_dataset().filter_rows(False)
bfile = new_temp_file(prefix='test_empty_bim')
hl.export_plink(mt, bfile, ind_id=mt.s)
with self.assertRaisesRegex(FatalError, "BIM file does not contain any variants"):
hl.import_plink(bfile + '.bed', bfile + '.bim', bfile + '.fam')
def test_import_plink_a1_major(self):
mt = get_dataset()
bfile = new_temp_file(prefix='sample_plink')
hl.export_plink(mt, bfile, ind_id=mt.s)
def get_data(a2_reference):
mt_imported = hl.import_plink(bfile + '.bed', bfile + '.bim', bfile + '.fam', a2_reference=a2_reference)
return hl.variant_qc(mt_imported).rows().key_by('rsid')
a2 = get_data(a2_reference=True)
a1 = get_data(a2_reference=False)
j = a2.annotate(a1_alleles=a1[a2.rsid].alleles, a1_vqc=a1[a2.rsid].variant_qc).rename(
{'variant_qc': 'a2_vqc', 'alleles': 'a2_alleles'}
)
self.assertTrue(
j.all(
(j.a1_alleles[0] == j.a2_alleles[1])
& (j.a1_alleles[1] == j.a2_alleles[0])
& (j.a1_vqc.n_not_called == j.a2_vqc.n_not_called)
& (j.a1_vqc.n_het == j.a2_vqc.n_het)
& (j.a1_vqc.homozygote_count[0] == j.a2_vqc.homozygote_count[1])
& (j.a1_vqc.homozygote_count[1] == j.a2_vqc.homozygote_count[0])
)
)
def test_import_plink_same_locus(self):
mt = hl.balding_nichols_model(n_populations=2, n_samples=10, n_variants=100)
mt = mt.key_rows_by(locus=hl.locus('1', 100, reference_genome='GRCh37'), alleles=mt.alleles).select_rows()
mt = mt.key_cols_by(s=hl.str(mt.sample_idx)).select_cols()
mt = mt.select_globals()
out = new_temp_file(prefix='plink')
hl.export_plink(mt, out)
mt2 = hl.import_plink(f'{out}.bed', f'{out}.bim', f'{out}.fam').select_cols().select_rows()
assert mt2._same(mt)
mt3 = hl.import_plink(f'{out}.bed', f'{out}.bim', f'{out}.fam', min_partitions=10).select_cols().select_rows()
assert mt3._same(mt)
def test_import_plink_partitions(self):
mt = hl.balding_nichols_model(n_populations=2, n_samples=10, n_variants=100)
mt = mt.select_rows()
mt = mt.key_cols_by(s=hl.str(mt.sample_idx)).select_cols()
mt = mt.select_globals()
out = new_temp_file(prefix='plink')
hl.export_plink(mt, out)
mt2 = hl.import_plink(f'{out}.bed', f'{out}.bim', f'{out}.fam', min_partitions=10).select_cols().select_rows()
assert mt2.n_partitions() == 10
assert mt2._same(mt)
def test_import_plink_contig_recoding_w_reference(self):
vcf = hl.split_multi_hts(
hl.import_vcf(
resource('sample2.vcf'), reference_genome=hl.get_reference('GRCh38'), contig_recoding={"22": "chr22"}
)
)
bfile = new_temp_file(prefix='sample_plink')
hl.export_plink(vcf, bfile)
plink = hl.import_plink(
bfile + '.bed',
bfile + '.bim',
bfile + '.fam',
a2_reference=True,
contig_recoding={'chr22': '22'},
reference_genome='GRCh37',
).rows()
self.assertTrue(plink.all(plink.locus.contig == "22"))
self.assertEqual(vcf.count_rows(), plink.count())
self.assertTrue(plink.locus.dtype, hl.tlocus('GRCh37'))
def test_import_plink_no_reference_specified(self):
bfile = resource('fastlmmTest')
plink = hl.import_plink(bfile + '.bed', bfile + '.bim', bfile + '.fam', reference_genome=None)
self.assertEqual(plink.locus.dtype, hl.tstruct(contig=hl.tstr, position=hl.tint32))
def test_import_plink_and_ignore_rows(self):
bfile = doctest_resource('ldsc')
plink = hl.import_plink(bfile + '.bed', bfile + '.bim', bfile + '.fam', block_size=16)
self.assertEqual(plink.aggregate_cols(hl.agg.count()), 489)
def test_import_plink_skip_invalid_loci(self):
mt = hl.import_plink(
resource('skip_invalid_loci.bed'),
resource('skip_invalid_loci.bim'),
resource('skip_invalid_loci.fam'),
reference_genome='GRCh37',
skip_invalid_loci=True,
contig_recoding={'chr1': '1'},
)
self.assertEqual(mt._force_count_rows(), 3)
with self.assertRaisesRegex(FatalError, 'Invalid locus'):
(
hl.import_plink(
resource('skip_invalid_loci.bed'),
resource('skip_invalid_loci.bim'),
resource('skip_invalid_loci.fam'),
)._force_count_rows()
)
@unittest.skipIf('HAIL_TEST_SKIP_PLINK' in os.environ, 'Skipping tests requiring plink')
def test_export_plink(self):
vcf_file = resource('sample.vcf')
mt = hl.split_multi_hts(hl.import_vcf(vcf_file, min_partitions=10))
# permute columns so not in alphabetical order!
import random
indices = list(range(mt.count_cols()))
random.shuffle(indices)
mt = mt.choose_cols(indices)
local_split_vcf_file = uri_path(new_local_temp_file())
local_hl_output = uri_path(new_local_temp_file())
plink_output = uri_path(new_local_temp_file())
merge_output = uri_path(new_local_temp_file())
with hl.TemporaryFilename() as split_vcf_file:
hl.export_vcf(mt, split_vcf_file)
hl.hadoop_copy(split_vcf_file, local_split_vcf_file)
with hl.TemporaryFilename() as hl_output:
hl.export_plink(mt, hl_output)
hl.hadoop_copy(hl_output + '.bed', local_hl_output + '.bed')
hl.hadoop_copy(hl_output + '.bim', local_hl_output + '.bim')
hl.hadoop_copy(hl_output + '.fam', local_hl_output + '.fam')
run_command(
[
"plink",
"--vcf",
local_split_vcf_file,
"--make-bed",
"--out",
plink_output,
"--const-fid",
"--keep-allele-order",
]