def test_concordance(self):
dataset = get_dataset()
glob_conc, cols_conc, rows_conc = hl.concordance(dataset, dataset)
self.assertEqual(sum([sum(glob_conc[i]) for i in range(5)]), dataset.count_rows() * dataset.count_cols())
counts = dataset.aggregate_entries(hl.Struct(n_het=agg.filter(dataset.GT.is_het(), agg.count()),
n_hom_ref=agg.filter(dataset.GT.is_hom_ref(),
agg.count()),
n_hom_var=agg.filter(dataset.GT.is_hom_var(),
agg.count()),
nNoCall=agg.filter(hl.is_missing(dataset.GT),
agg.count())))
self.assertEqual(glob_conc[0][0], 0)
self.assertEqual(glob_conc[1][1], counts.nNoCall)
self.assertEqual(glob_conc[2][2], counts.n_hom_ref)
self.assertEqual(glob_conc[3][3], counts.n_het)
self.assertEqual(glob_conc[4][4], counts.n_hom_var)
[self.assertEqual(glob_conc[i][j], 0) for i in range(5) for j in range(5) if i != j]
self.assertTrue(cols_conc.all(hl.sum(hl.flatten(cols_conc.concordance)) == dataset.count_rows()))
self.assertTrue(rows_conc.all(hl.sum(hl.flatten(rows_conc.concordance)) == dataset.count_cols()))
cols_conc.write('/tmp/foo.kt', overwrite=True)
rows_conc.write('/tmp/foo.kt', overwrite=True)
def test_concordance(self):
dataset = get_dataset()
glob_conc, cols_conc, rows_conc = hl.concordance(dataset, dataset)
self.assertEqual(sum([sum(glob_conc[i]) for i in range(5)]), dataset.count_rows() * dataset.count_cols())
counts = dataset.aggregate_entries(hl.Struct(n_het=agg.filter(dataset.GT.is_het(), agg.count()),
n_hom_ref=agg.filter(dataset.GT.is_hom_ref(),
agg.count()),
n_hom_var=agg.filter(dataset.GT.is_hom_var(),
agg.count()),
nNoCall=agg.filter(hl.is_missing(dataset.GT),
agg.count())))
self.assertEqual(glob_conc[0][0], 0)
self.assertEqual(glob_conc[1][1], counts.nNoCall)
self.assertEqual(glob_conc[2][2], counts.n_hom_ref)
self.assertEqual(glob_conc[3][3], counts.n_het)
self.assertEqual(glob_conc[4][4], counts.n_hom_var)
[self.assertEqual(glob_conc[i][j], 0) for i in range(5) for j in range(5) if i != j]
self.assertTrue(cols_conc.all(hl.sum(hl.flatten(cols_conc.concordance)) == dataset.count_rows()))
self.assertTrue(rows_conc.all(hl.sum(hl.flatten(rows_conc.concordance)) == dataset.count_cols()))
cols_conc.write('/tmp/foo.kt', overwrite=True)
rows_conc.write('/tmp/foo.kt', overwrite=True)
def combine(ts):
# pylint: disable=protected-access
tmp = ts.annotate(
alleles=merge_alleles(ts.data.map(lambda d: d.alleles)),
rsid=hl.find(hl.is_defined, ts.data.map(lambda d: d.rsid)),
filters=hl.set(hl.flatten(ts.data.map(lambda d: hl.array(d.filters)))),
info=hl.struct(
DP=hl.sum(ts.data.map(lambda d: d.info.DP)),
MQ_DP=hl.sum(ts.data.map(lambda d: d.info.MQ_DP)),
QUALapprox=hl.sum(ts.data.map(lambda d: d.info.QUALapprox)),
RAW_MQ=hl.sum(ts.data.map(lambda d: d.info.RAW_MQ)),
VarDP=hl.sum(ts.data.map(lambda d: d.info.VarDP)),
SB=hl.array([
hl.sum(ts.data.map(lambda d: d.info.SB[0])),
hl.sum(ts.data.map(lambda d: d.info.SB[1])),
hl.sum(ts.data.map(lambda d: d.info.SB[2])),
hl.sum(ts.data.map(lambda d: d.info.SB[3]))
])))
tmp = tmp.annotate(
__entries=hl.bind(
lambda combined_allele_index:
hl.range(0, hl.len(tmp.data)).flatmap(
lambda i:
hl.cond(hl.is_missing(tmp.data[i].__entries),
hl.range(0, hl.len(tmp.g[i].__cols))
.map(lambda _: hl.null(tmp.data[i].__entries.dtype.element_type)),
hl.bind(
lambda old_to_new: tmp.data[i].__entries.map(lambda e: renumber_entry(e, old_to_new)),
hl.range(0, hl.len(tmp.data[i].alleles)).map(
lambda j: combined_allele_index[tmp.data[i].alleles[j]])))),
hl.dict(hl.range(0, hl.len(tmp.alleles)).map(
lambda j: hl.tuple([tmp.alleles[j], j])))))
tmp = tmp.annotate_globals(__cols=hl.flatten(tmp.g.map(lambda g: g.__cols)))
return tmp.drop('data', 'g')
def merge_alleles(alleles):
from hail.expr.functions import _num_allele_type, _allele_ints
return hl.rbind(
alleles.map(lambda a: hl.or_else(a[0], ''))
.fold(lambda s, t: hl.cond(hl.len(s) > hl.len(t), s, t), ''),
lambda ref:
hl.rbind(
alleles.map(
lambda al: hl.rbind(
al[0],
lambda r:
hl.array([ref]).extend(
al[1:].map(
lambda a:
hl.rbind(
_num_allele_type(r, a),
lambda at:
hl.cond(
(_allele_ints['SNP'] == at) |
(_allele_ints['Insertion'] == at) |
(_allele_ints['Deletion'] == at) |
(_allele_ints['MNP'] == at) |
(_allele_ints['Complex'] == at),
a + ref[hl.len(r):],
a)))))),
lambda lal:
hl.struct(
globl=hl.array([ref]).extend(hl.array(hl.set(hl.flatten(lal)).remove(ref))),
local=lal)))
def sor_from_sb(
sb: Union[hl.expr.ArrayNumericExpression, hl.expr.ArrayExpression]
) -> hl.expr.Float64Expression:
"""
Computes `SOR` (Symmetric Odds Ratio test) annotation from the `SB` (strand balance table) field.
.. note::
This function can either take
- an array of length four containing the forward and reverse strands' counts of ref and alt alleles: [ref fwd, ref rev, alt fwd, alt rev]
- a two dimensional array with arrays of length two, containing the counts: [[ref fwd, ref rev], [alt fwd, alt rev]]
GATK code here: https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatio.java
:param sb: Count of ref/alt reads on each strand
:return: SOR value
"""
if not isinstance(sb, hl.expr.ArrayNumericExpression):
sb = hl.bind(lambda x: hl.flatten(x), sb)
sb = sb.map(lambda x: hl.float64(x) + 1)
ref_fw = sb[0]
ref_rv = sb[1]
alt_fw = sb[2]
alt_rv = sb[3]
symmetrical_ratio = ((ref_fw * alt_rv) / (alt_fw * ref_rv)) + (
(alt_fw * ref_rv) / (ref_fw * alt_rv)
)
ref_ratio = hl.min(ref_rv, ref_fw) / hl.max(ref_rv, ref_fw)
alt_ratio = hl.min(alt_fw, alt_rv) / hl.max(alt_fw, alt_rv)
sor = hl.log(symmetrical_ratio) + hl.log(ref_ratio) - hl.log(alt_ratio)
return sor
def merge_alleles(alleles):
from hail.expr.functions import _num_allele_type, _allele_ints
return hl.rbind(
alleles.map(lambda a: hl.or_else(a[0], ''))
.fold(lambda s, t: hl.cond(hl.len(s) > hl.len(t), s, t), ''),
lambda ref:
hl.rbind(
alleles.map(
lambda al: hl.rbind(
al[0],
lambda r:
hl.array([ref]).extend(
al[1:].map(
lambda a:
hl.rbind(
_num_allele_type(r, a),
lambda at:
hl.cond(
(_allele_ints['SNP'] == at) |
(_allele_ints['Insertion'] == at) |
(_allele_ints['Deletion'] == at) |
(_allele_ints['MNP'] == at) |
(_allele_ints['Complex'] == at),
a + ref[hl.len(r):],
a)))))),
lambda lal:
hl.struct(
globl=hl.array([ref]).extend(hl.array(hl.set(hl.flatten(lal)).remove(ref))),
local=lal)))
def combine(ts):
# pylint: disable=protected-access
tmp = ts.annotate(
alleles=merge_alleles(ts.data.map(lambda d: d.alleles)),
rsid=hl.find(hl.is_defined, ts.data.map(lambda d: d.rsid)),
info=hl.struct(
MQ_DP=hl.sum(ts.data.map(lambda d: d.info.MQ_DP)),
QUALapprox=hl.sum(ts.data.map(lambda d: d.info.QUALapprox)),
RAW_MQ=hl.sum(ts.data.map(lambda d: d.info.RAW_MQ)),
VarDP=hl.sum(ts.data.map(lambda d: d.info.VarDP)),
SB_TABLE=hl.array([
hl.sum(ts.data.map(lambda d: d.info.SB_TABLE[0])),
hl.sum(ts.data.map(lambda d: d.info.SB_TABLE[1])),
hl.sum(ts.data.map(lambda d: d.info.SB_TABLE[2])),
hl.sum(ts.data.map(lambda d: d.info.SB_TABLE[3]))
])))
tmp = tmp.annotate(
__entries=hl.bind(
lambda combined_allele_index:
hl.range(0, hl.len(tmp.data)).flatmap(
lambda i:
hl.cond(hl.is_missing(tmp.data[i].__entries),
hl.range(0, hl.len(tmp.g[i].__cols))
.map(lambda _: hl.null(tmp.data[i].__entries.dtype.element_type)),
hl.bind(
lambda old_to_new: tmp.data[i].__entries.map(lambda e: renumber_entry(e, old_to_new)),
hl.array([0]).extend(
hl.range(0, hl.len(tmp.data[i].alleles)).map(
lambda j: combined_allele_index[tmp.data[i].alleles[j]]))))),
hl.dict(hl.range(1, hl.len(tmp.alleles) + 1).map(
lambda j: hl.tuple([tmp.alleles[j - 1], j])))))
tmp = tmp.annotate_globals(__cols=hl.flatten(tmp.g.map(lambda g: g.__cols)))
return tmp.drop('data', 'g')
def combine(ts):
def merge_alleles(alleles):
from hail.expr.functions import _num_allele_type, _allele_ints
return hl.rbind(
alleles.map(lambda a: hl.or_else(a[0], '')).fold(
lambda s, t: hl.cond(hl.len(s) > hl.len(t), s, t), ''),
lambda ref: hl.rbind(
alleles.map(lambda al: hl.rbind(
al[0], lambda r: hl.array([ref]).
extend(al[1:].map(lambda a: hl.rbind(
_num_allele_type(r, a), lambda at: hl.cond(
(_allele_ints['SNP'] == at)
| (_allele_ints['Insertion'] == at)
| (_allele_ints['Deletion'] == at)
| (_allele_ints['MNP'] == at)
| (_allele_ints['Complex'] == at), a + ref[hl.len(
r):], a)))))), lambda lal: hl.
struct(globl=hl.array([ref]).extend(
hl.array(hl.set(hl.flatten(lal)).remove(ref))),
local=lal)))
def renumber_entry(entry, old_to_new) -> StructExpression:
# global index of alternate (non-ref) alleles
return entry.annotate(LA=entry.LA.map(lambda lak: old_to_new[lak]))
if (ts.row.dtype, ts.globals.dtype) not in _merge_function_map:
f = hl.experimental.define_function(
lambda row, gbl: hl.rbind(
merge_alleles(row.data.map(lambda d: d.alleles)), lambda
alleles: hl.struct(
locus=row.locus,
alleles=alleles.globl,
rsid=hl.find(hl.is_defined, row.data.map(lambda d: d.rsid)
),
__entries=hl.bind(
lambda combined_allele_index: hl.
range(0, hl.len(row.data)).flatmap(lambda i: hl.cond(
hl.is_missing(row.data[i].__entries),
hl.range(0, hl.len(gbl.g[i].__cols)).map(
lambda _: hl.null(row.data[i].__entries.dtype.
element_type)),
hl.bind(
lambda old_to_new: row.data[i].__entries.map(
lambda e: renumber_entry(e, old_to_new)),
hl.range(0, hl.len(alleles.local[i])).map(
lambda j: combined_allele_index[
alleles.local[i][j]])))),
hl.dict(
hl.range(0, hl.len(alleles.globl)).map(
lambda j: hl.tuple([alleles.globl[j], j])))))),
ts.row.dtype, ts.globals.dtype)
_merge_function_map[(ts.row.dtype, ts.globals.dtype)] = f
merge_function = _merge_function_map[(ts.row.dtype, ts.globals.dtype)]
ts = Table(
TableMapRows(
ts._tir,
Apply(merge_function._name, merge_function._ret_type,
TopLevelReference('row'), TopLevelReference('global'))))
return ts.transmute_globals(
__cols=hl.flatten(ts.g.map(lambda g: g.__cols)))
def multi_way_union_mts(mts: list, tmp_dir: str,
chunk_size: int) -> hl.MatrixTable:
"""Joins MatrixTables in the provided list
:param list mts: list of MatrixTables to join together
:param str tmp_dir: path to temporary directory for intermediate results
:param int chunk_size: number of MatrixTables to join per chunk
:return: joined MatrixTable
:rtype: MatrixTable
"""
staging = [mt.localize_entries("__entries", "__cols") for mt in mts]
stage = 0
while len(staging) > 1:
n_jobs = int(math.ceil(len(staging) / chunk_size))
info(f"multi_way_union_mts: stage {stage}: {n_jobs} total jobs")
next_stage = []
for i in range(n_jobs):
to_merge = staging[chunk_size * i:chunk_size * (i + 1)]
info(
f"multi_way_union_mts: stage {stage} / job {i}: merging {len(to_merge)} inputs"
)
merged = hl.Table.multi_way_zip_join(to_merge, "__entries",
"__cols")
merged = merged.annotate(__entries=hl.flatten(
hl.range(hl.len(merged.__entries)).map(lambda i: hl.coalesce(
merged.__entries[i].__entries,
hl.range(hl.len(merged.__cols[i].__cols)).map(
lambda j: hl.null(merged.__entries.__entries.dtype.
element_type.element_type)),
))))
merged = merged.annotate_globals(
__cols=hl.flatten(merged.__cols.map(lambda x: x.__cols)))
next_stage.append(
merged.checkpoint(os.path.join(tmp_dir,
f"stage_{stage}_job_{i}.ht"),
overwrite=True))
info(f"done stage {stage}")
stage += 1
staging.clear()
staging.extend(next_stage)
return (staging[0]._unlocalize_entries(
"__entries", "__cols", list(mts[0].col_key)).unfilter_entries())
def combine_r(ts):
if (ts.row.dtype, ts.globals.dtype) not in _merge_function_map:
f = hl.experimental.define_function(
lambda row, gbl:
hl.struct(
locus=row.locus,
ref_allele=hl.find(hl.is_defined, row.data.map(lambda d: d.ref_allele)),
__entries=hl.range(0, hl.len(row.data)).flatmap(
lambda i:
hl.if_else(hl.is_missing(row.data[i]),
hl.range(0, hl.len(gbl.g[i].__cols))
.map(lambda _: hl.missing(row.data[i].__entries.dtype.element_type)),
row.data[i].__entries))),
ts.row.dtype, ts.globals.dtype)
_merge_function_map[(ts.row.dtype, ts.globals.dtype)] = f
merge_function = _merge_function_map[(ts.row.dtype, ts.globals.dtype)]
ts = Table(TableMapRows(ts._tir, Apply(merge_function._name,
merge_function._ret_type,
TopLevelReference('row'),
TopLevelReference('global'))))
return ts.transmute_globals(__cols=hl.flatten(ts.g.map(lambda g: g.__cols)))
def combine(ts):
def merge_alleles(alleles):
from hail.expr.functions import _num_allele_type, _allele_ints
return hl.rbind(
alleles.map(lambda a: hl.or_else(a[0], ''))
.fold(lambda s, t: hl.cond(hl.len(s) > hl.len(t), s, t), ''),
lambda ref:
hl.rbind(
alleles.map(
lambda al: hl.rbind(
al[0],
lambda r:
hl.array([ref]).extend(
al[1:].map(
lambda a:
hl.rbind(
_num_allele_type(r, a),
lambda at:
hl.cond(
(_allele_ints['SNP'] == at) |
(_allele_ints['Insertion'] == at) |
(_allele_ints['Deletion'] == at) |
(_allele_ints['MNP'] == at) |
(_allele_ints['Complex'] == at),
a + ref[hl.len(r):],
a)))))),
lambda lal:
hl.struct(
globl=hl.array([ref]).extend(hl.array(hl.set(hl.flatten(lal)).remove(ref))),
local=lal)))
def renumber_entry(entry, old_to_new) -> StructExpression:
# global index of alternate (non-ref) alleles
return entry.annotate(LA=entry.LA.map(lambda lak: old_to_new[lak]))
if (ts.row.dtype, ts.globals.dtype) not in _merge_function_map:
f = hl.experimental.define_function(
lambda row, gbl:
hl.rbind(
merge_alleles(row.data.map(lambda d: d.alleles)),
lambda alleles:
hl.struct(
locus=row.locus,
alleles=alleles.globl,
rsid=hl.find(hl.is_defined, row.data.map(lambda d: d.rsid)),
__entries=hl.bind(
lambda combined_allele_index:
hl.range(0, hl.len(row.data)).flatmap(
lambda i:
hl.cond(hl.is_missing(row.data[i].__entries),
hl.range(0, hl.len(gbl.g[i].__cols))
.map(lambda _: hl.null(row.data[i].__entries.dtype.element_type)),
hl.bind(
lambda old_to_new: row.data[i].__entries.map(
lambda e: renumber_entry(e, old_to_new)),
hl.range(0, hl.len(alleles.local[i])).map(
lambda j: combined_allele_index[alleles.local[i][j]])))),
hl.dict(hl.range(0, hl.len(alleles.globl)).map(
lambda j: hl.tuple([alleles.globl[j], j])))))),
ts.row.dtype, ts.globals.dtype)
_merge_function_map[(ts.row.dtype, ts.globals.dtype)] = f
merge_function = _merge_function_map[(ts.row.dtype, ts.globals.dtype)]
ts = Table(TableMapRows(ts._tir, Apply(merge_function._name,
TopLevelReference('row'),
TopLevelReference('global'))))
return ts.transmute_globals(__cols=hl.flatten(ts.g.map(lambda g: g.__cols)))
'f7': 'phase',
'f8': 'attributes'
})
ht_transcripts = ht_transcripts.filter(
ht_transcripts.feature_type == 'transcript')
ht_transcripts = ht_transcripts.annotate(interval=hl.interval(
hl.locus(ht_transcripts.contig, ht_transcripts.start, 'GRCh37'),
hl.locus(ht_transcripts.contig, ht_transcripts.end + 1, 'GRCh37')))
ht_transcripts = ht_transcripts.annotate(attributes=hl.dict(
hl.map(
lambda x: (x.split(' ')[0], x.split(' ')[1].replace('"', '').replace(
';$', '')), ht_transcripts.attributes.split('; '))))
attribute_cols = list(
ht_transcripts.aggregate(
hl.set(hl.flatten(hl.agg.collect(ht_transcripts.attributes.keys())))))
ht_transcripts = ht_transcripts.annotate(
**{
x: hl.or_missing(ht_transcripts.attributes.contains(x),
ht_transcripts.attributes[x])
for x in attribute_cols
})
ht_transcripts = ht_transcripts.select(*([
'transcript_id', 'transcript_name', 'transcript_type', 'strand',
'transcript_status', 'havana_transcript', 'ccdsid', 'ont', 'gene_name',
'interval', 'gene_type', 'annotation_source', 'havana_gene', 'gene_status',
'tag'
]))
ht_transcripts = ht_transcripts.rename({
'havana_transcript': 'havana_transcript_id',
'havana_gene': 'havana_gene_id'
def merge_alleles(alleles) -> ArrayExpression:
# alleles is tarray(tarray(tstruct(ref=tstr, alt=tstr)))
return hl.rbind(hl.array(hl.set(hl.flatten(alleles))),
lambda arr:
hl.filter(lambda a: a.alt != '<NON_REF>', arr)
.extend(hl.filter(lambda a: a.alt == '<NON_REF>', arr)))
def compute_from_vp_mt(chr20: bool, overwrite: bool):
meta = get_gnomad_meta('exomes')
vp_mt = hl.read_matrix_table(full_mt_path('exomes'))
vp_mt = vp_mt.filter_cols(meta[vp_mt.col_key].release)
ann_ht = hl.read_table(vp_ann_ht_path('exomes'))
phase_ht = hl.read_table(phased_vp_count_ht_path('exomes'))
if chr20:
vp_mt, ann_ht, phase_ht = filter_to_chr20([vp_mt, ann_ht, phase_ht])
vep1_expr = get_worst_gene_csq_code_expr(ann_ht.vep1)
vep2_expr = get_worst_gene_csq_code_expr(ann_ht.vep2)
ann_ht = ann_ht.select(
'snv1',
'snv2',
is_singleton_vp=(ann_ht.freq1['all'].AC < 2) & (ann_ht.freq2['all'].AC < 2),
pop_af=hl.dict(
ann_ht.freq1.key_set().intersection(ann_ht.freq2.key_set())
.map(
lambda pop: hl.tuple([pop, hl.max(ann_ht.freq1[pop].AF, ann_ht.freq2[pop].AF)])
)
),
popmax_af=hl.max(ann_ht.popmax1.AF, ann_ht.popmax2.AF, filter_missing=False),
filtered=(hl.len(ann_ht.filters1) > 0) | (hl.len(ann_ht.filters2) > 0),
vep=vep1_expr.keys().filter(
lambda k: vep2_expr.contains(k)
).map(
lambda k: vep1_expr[k].annotate(
csq=hl.max(vep1_expr[k].csq, vep2_expr[k].csq)
)
)
)
vp_mt = vp_mt.annotate_cols(
pop=meta[vp_mt.col_key].pop
)
vp_mt = vp_mt.annotate_rows(
**ann_ht[vp_mt.row_key],
phase_info=phase_ht[vp_mt.row_key].phase_info
)
vp_mt = vp_mt.filter_rows(
~vp_mt.filtered
)
vp_mt = vp_mt.filter_entries(
vp_mt.GT1.is_het() & vp_mt.GT2.is_het() & vp_mt.adj1 & vp_mt.adj2
)
vp_mt = vp_mt.select_entries(
x=True
)
vp_mt = vp_mt.annotate_cols(
pop=['all', vp_mt.pop]
)
vp_mt = vp_mt.explode_cols('pop')
vp_mt = vp_mt.explode_rows('vep')
vp_mt = vp_mt.transmute_rows(
**vp_mt.vep
)
def get_grouped_phase_agg():
return hl.agg.group_by(
hl.case()
.when(~vp_mt.is_singleton_vp & (vp_mt.phase_info[vp_mt.pop].em.adj.p_chet > CHET_THRESHOLD), 1)
.when(~vp_mt.is_singleton_vp & (vp_mt.phase_info[vp_mt.pop].em.adj.p_chet < SAME_HAP_THRESHOLD), 2)
.default(3)
,
hl.agg.min(vp_mt.csq)
)
vp_mt = vp_mt.group_rows_by(
'gene_id',
'gene_symbol'
).aggregate(
all=hl.agg.filter(
vp_mt.x &
hl.if_else(
vp_mt.pop == 'all',
hl.is_defined(vp_mt.popmax_af) &
(vp_mt.popmax_af <= MAX_FREQ),
vp_mt.pop_af[vp_mt.pop] <= MAX_FREQ
),
get_grouped_phase_agg()
),
af_le_0_001=hl.agg.filter(
hl.if_else(
vp_mt.pop == 'all',
hl.is_defined(vp_mt.popmax_af) &
(vp_mt.popmax_af <= 0.001),
vp_mt.pop_af[vp_mt.pop] <= 0.001
)
& vp_mt.x,
get_grouped_phase_agg()
)
)
vp_mt = vp_mt.checkpoint('gs://gnomad-tmp/compound_hets/chet_per_gene{}.2.mt'.format(
'.chr20' if chr20 else ''
), overwrite=True)
gene_ht = vp_mt.annotate_rows(
row_counts=hl.flatten([
hl.array(
hl.agg.group_by(
vp_mt.pop,
hl.struct(
csq=csq,
af=af,
# TODO: Review this
# These will only kept the worst csq -- now maybe it'd be better to keep either
# - the worst csq for chet or
# - the worst csq for both chet and same_hap
n_worst_chet=hl.agg.count_where(vp_mt[af].get(1) == csq_i),
n_chet=hl.agg.count_where((vp_mt[af].get(1) == csq_i) & (vp_mt[af].get(2, 9) >= csq_i) & (vp_mt[af].get(3, 9) >= csq_i)),
n_same_hap=hl.agg.count_where((vp_mt[af].get(2) == csq_i) & (vp_mt[af].get(1, 9) > csq_i) & (vp_mt[af].get(3, 9) >= csq_i)),
n_unphased=hl.agg.count_where((vp_mt[af].get(3) == csq_i) & (vp_mt[af].get(1, 9) > csq_i) & (vp_mt[af].get(2, 9) > csq_i))
)
)
).filter(
lambda x: (x[1].n_chet > 0) | (x[1].n_same_hap > 0) | (x[1].n_unphased > 0)
).map(
lambda x: x[1].annotate(
pop=x[0]
)
)
for csq_i, csq in enumerate(CSQ_CODES)
for af in ['all', 'af_le_0_001']
])
).rows()
gene_ht = gene_ht.explode('row_counts')
gene_ht = gene_ht.select(
**gene_ht.row_counts
)
gene_ht.describe()
gene_ht = gene_ht.checkpoint(
'gs://gnomad-lfran/compound_hets/chet_per_gene{}.ht'.format(
'.chr20' if chr20 else ''
),
overwrite=overwrite
)
gene_ht.flatten().export(
'gs://gnomad-lfran/compound_hets/chet_per_gene{}.tsv.gz'.format(
'.chr20' if chr20 else ''
)
)
def compute_from_full_mt(chr20: bool, overwrite: bool):
mt = get_gnomad_data('exomes', adj=True, release_samples=True)
freq_ht = hl.read_table(annotations_ht_path('exomes', 'frequencies'))
vep_ht = hl.read_table(annotations_ht_path('exomes', 'vep'))
rf_ht = hl.read_table(annotations_ht_path('exomes', 'rf'))
if chr20:
mt, freq_ht, vep_ht, rf_ht = filter_to_chr20([mt, freq_ht, vep_ht, rf_ht])
vep_ht = vep_ht.annotate(
vep=get_worst_gene_csq_code_expr(vep_ht.vep).values()
)
freq_ht = freq_ht.select(
freq=freq_ht.freq[:10],
popmax=freq_ht.popmax
)
freq_meta = hl.eval(freq_ht.globals.freq_meta)
freq_dict = {f['pop']: i for i, f in enumerate(freq_meta[:10]) if 'pop' in f}
freq_dict['all'] = 0
freq_dict = hl.literal(freq_dict)
mt = mt.annotate_rows(
**freq_ht[mt.row_key],
vep=vep_ht[mt.row_key].vep,
filters=rf_ht[mt.row_key].filters
)
mt = mt.filter_rows(
(mt.freq[0].AF <= MAX_FREQ) &
(hl.len(mt.vep) > 0) &
(hl.len(mt.filters) == 0)
)
mt = mt.filter_entries(mt.GT.is_non_ref())
mt = mt.select_entries(
is_het=mt.GT.is_het()
)
mt = mt.explode_rows(mt.vep)
mt = mt.transmute_rows(**mt.vep)
mt = mt.annotate_cols(
pop=['all', mt.meta.pop]
)
mt = mt.explode_cols(mt.pop)
mt = mt.group_rows_by(
'gene_id'
).aggregate_rows(
gene_symbol=hl.agg.take(mt.gene_symbol, 1)[0]
).aggregate(
counts=hl.agg.filter(
hl.if_else(
mt.pop == 'all',
hl.is_defined(mt.popmax) & (mt.popmax.AF <= MAX_FREQ),
mt.freq[freq_dict[mt.pop]].AF <= MAX_FREQ
),
hl.agg.group_by(
hl.if_else(
mt.pop == 'all',
mt.popmax.AF > 0.001,
mt.freq[freq_dict[mt.pop]].AF > 0.001
),
hl.struct(
hom_csq=hl.agg.filter(~mt.is_het, hl.agg.min(mt.csq)),
het_csq=hl.agg.filter(mt.is_het, hl.agg.min(mt.csq)),
het_het_csq=hl.sorted(
hl.array(
hl.agg.filter(mt.is_het, hl.agg.counter(mt.csq))
),
key=lambda x: x[0]
).scan(
lambda i, j: (j[0], i[1] + j[1]),
(0, 0)
).find(
lambda x: x[1] > 1
)[0]
)
)
)
)
mt = mt.annotate_entries(
counts=hl.struct(
all=hl.struct(
hom_csq=hl.min(mt.counts.get(True).hom_csq, mt.counts.get(False).hom_csq),
het_csq=hl.min(mt.counts.get(True).het_csq, mt.counts.get(False).het_csq),
het_het_csq=hl.min(
mt.counts.get(True).het_het_csq,
mt.counts.get(False).het_het_csq,
hl.or_missing(
hl.is_defined(mt.counts.get(True).het_csq) & hl.is_defined(mt.counts.get(False).het_csq),
hl.max(mt.counts.get(True).het_csq, mt.counts.get(False).het_csq)
)
),
),
af_le_0_001=mt.counts.get(False)
)
)
mt = mt.checkpoint('gs://gnomad-tmp/compound_hets/het_and_hom_per_gene{}.1.mt'.format(
'.chr20' if chr20 else ''
), overwrite=True)
gene_ht = mt.annotate_rows(
row_counts=hl.flatten([
hl.array(
hl.agg.group_by(
mt.pop,
hl.struct(
csq=csq,
af=af,
n_hom=hl.agg.count_where(mt.counts[af].hom_csq == csq_i),
n_het=hl.agg.count_where(mt.counts[af].het_csq == csq_i),
n_het_het=hl.agg.count_where(mt.counts[af].het_het_csq == csq_i)
)
)
).filter(
lambda x: (x[1].n_het > 0) | (x[1].n_hom > 0) | (x[1].n_het_het > 0)
).map(
lambda x: x[1].annotate(
pop=x[0]
)
)
for csq_i, csq in enumerate(CSQ_CODES)
for af in ['all', 'af_le_0_001']
])
).rows()
gene_ht = gene_ht.explode('row_counts')
gene_ht = gene_ht.select(
'gene_symbol',
**gene_ht.row_counts
)
gene_ht.describe()
gene_ht = gene_ht.checkpoint(
'gs://gnomad-lfran/compound_hets/het_and_hom_per_gene{}.ht'.format(
'.chr20' if chr20 else ''
),
overwrite=overwrite
)
gene_ht.flatten().export('gs://gnomad-lfran/compound_hets/het_and_hom_per_gene{}.tsv.gz'.format(
'.chr20' if chr20 else ''
))
def segment_intervals(ht, points):
"""Segment the interval keys of `ht` at a given set of points.
Parameters
----------
ht : :class:`.Table`
Table with interval keys.
points : :class:`.Table` or :class:`.ArrayExpression`
Points at which to segment the intervals, a table or an array.
Returns
-------
:class:`.Table`
"""
if len(ht.key) != 1 or not isinstance(ht.key[0].dtype, hl.tinterval):
raise ValueError(
"'segment_intervals' expects a table with interval keys")
point_type = ht.key[0].dtype.point_type
if isinstance(points, Table):
if len(points.key) != 1 or points.key[0].dtype != point_type:
raise ValueError(
"'segment_intervals' expects points to be a table with a single"
" key of the same type as the intervals in 'ht', or an array of those points:"
f"\n expect {point_type}, found {list(points.key.dtype.values())}"
)
points = hl.array(hl.set(points.collect(_localize=False)))
if points.dtype.element_type != point_type:
raise ValueError(
f"'segment_intervals' expects points to be a table with a single"
f" key of the same type as the intervals in 'ht', or an array of those points:"
f"\n expect {point_type}, found {points.dtype.element_type}")
points = hl._sort_by(points, lambda l, r: hl._compare(l, r) < 0)
ht = ht.annotate_globals(__points=points)
interval = ht.key[0]
points = ht.__points
lower = hl.expr.functions._lower_bound(points, interval.start)
higher = hl.expr.functions._lower_bound(points, interval.end)
n_points = hl.len(points)
lower = hl.if_else((lower < n_points) & (points[lower] == interval.start),
lower + 1, lower)
higher = hl.if_else((higher < n_points) & (points[higher] == interval.end),
higher - 1, higher)
interval_results = hl.rbind(
lower, higher, lambda lower, higher: hl.cond(
lower >= higher, [interval],
hl.flatten([
[
hl.interval(interval.start,
points[lower],
includes_start=interval.includes_start,
includes_end=False)
],
hl.range(lower, higher - 1).map(lambda x: hl.interval(
points[x],
points[x + 1],
includes_start=True,
includes_end=False)),
[
hl.interval(points[higher - 1],
interval.end,
includes_start=True,
includes_end=interval.includes_end)
],
])))
ht = ht.annotate(__new_intervals=interval_results,
lower=lower,
higher=higher).explode('__new_intervals')
return ht.key_by(**{
list(ht.key)[0]: ht.__new_intervals
}).drop('__new_intervals')
'SMRRNANM',
'SMVQCFL',
'SMTRSCPT',
'SMMPPDPR',
'SMCGLGTH',
'SMUNPDRD',
'SMMPPDUN',
'SME2ANTI',
'SMALTALG',
'SME2SNSE',
'SMMFLGTH',
'SMSPLTRD',
'SME1ANTI',
'SME1SNSE',
'SMNUM5CD']
ht_samples = ht_samples.annotate(**{x: hl.float(ht_samples[x]) for x in float_cols})
ht_samples = ht_samples.annotate(**{x: hl.int(ht_samples[x].replace('.0$', '')) for x in int_cols})
ht = ht.filter(ht.feature_type == 'gene')
ht = ht.annotate(interval=hl.interval(hl.locus(ht['contig'], ht['start'], 'GRCh37'), hl.locus(ht['contig'], ht['end'] + 1, 'GRCh37')))
ht = ht.annotate(attributes=hl.dict(hl.map(lambda x: (x.split(' ')[0], x.split(' ')[1].replace('"', '').replace(';$', '')), ht['attributes'].split('; '))))
attribute_cols = list(ht.aggregate(hl.set(hl.flatten(hl.agg.collect(ht.attributes.keys())))))
ht = ht.annotate(**{x: hl.or_missing(ht_genes.attributes.contains(x), ht_genes.attributes[x]) for x in attribute_cols})
ht = ht.select(*(['gene_id', 'interval', 'gene_type', 'strand', 'annotation_source', 'havana_gene', 'gene_status', 'tag']))
ht = ht.rename({'havana_gene': 'havana_gene_id'})
ht = ht.key_by(ht_genes.gene_id)
"""
def import_gtf(path, key=None):
"""Import a GTF file.
The GTF file format is identical to the GFF version 2 file format,
and so this function can be used to import GFF version 2 files as
well.
See https://www.ensembl.org/info/website/upload/gff.html for more
details on the GTF/GFF2 file format.
The :class:`.Table` returned by this function will include the following
row fields:
.. code-block:: text
'seqname': str
'source': str
'feature': str
'start': int32
'end': int32
'score': float64
'strand': str
'frame': int32
There will also be corresponding fields for every tag found in the
attribute field of the GTF file.
.. note::
The "end" field in the table will be incremented by 1 in
comparison to the value found in the GTF file, as the end
coordinate in a GTF file is inclusive while the end
coordinate in Hail is exclusive.
Example
-------
>>> ht = hl.experimental.import_gtf('data/test.gtf', key='gene_id')
>>> ht.describe()
.. code-block:: text
----------------------------------------
Global fields:
None
----------------------------------------
Row fields:
'seqname': str
'source': str
'feature': str
'start': int32
'end': int32
'score': float64
'strand': str
'frame': int32
'havana_gene': str
'exon_id': str
'havana_transcript': str
'transcript_name': str
'gene_type': str
'tag': str
'transcript_status': str
'exon_number': str
'level': str
'transcript_id': str
'transcript_type': str
'gene_id': str
'gene_name': str
'gene_status': str
----------------------------------------
Key: ['gene_id']
----------------------------------------
Parameters
----------
path : :obj:`str`
File to import.
key : :obj:`str` or :obj:`list` of :obj:`str`
Key field(s). Can be tag name(s) found in the attribute field
of the GTF file.
Returns
-------
:class:`.Table`
"""
ht = hl.import_table(path,
comment='#',
no_header=True,
types={'f3': hl.tint,
'f4': hl.tint,
'f5': hl.tfloat,
'f7': hl.tint},
missing='.',
delimiter='\t')
ht = ht.rename({'f0': 'seqname',
'f1': 'source',
'f2': 'feature',
'f3': 'start',
'f4': 'end',
'f5': 'score',
'f6': 'strand',
'f7': 'frame',
'f8': 'attribute'})
ht = ht.annotate(end=ht['end'] + 1)
ht = ht.annotate(attribute=hl.dict(
hl.map(lambda x: (x.split(' ')[0],
x.split(' ')[1].replace('"', '').replace(';$', '')),
ht['attribute'].split('; '))))
attributes = list(ht.aggregate(
hl.set(hl.flatten(hl.agg.collect(ht['attribute'].keys())))))
ht = ht.annotate(**{x: hl.or_missing(ht['attribute'].contains(x),
ht['attribute'][x])
for x in attributes})
ht = ht.drop(ht['attribute'])
if key:
key = wrap_to_list(key)
ht = ht.key_by(*key)
return ht
def merge_alleles(alleles) -> ArrayExpression:
return hl.array(hl.set(hl.flatten(alleles)))
def merge_alleles(alleles) -> ArrayExpression:
return hl.array(hl.set(hl.flatten(alleles)))
def fs_from_sb(
sb: Union[hl.expr.ArrayNumericExpression, hl.expr.ArrayExpression],
normalize: bool = True,
min_cell_count: int = 200,
min_count: int = 4,
min_p_value: float = 1e-320,
) -> hl.expr.Int64Expression:
"""
Computes `FS` (Fisher strand balance) annotation from the `SB` (strand balance table) field.
`FS` is the phred-scaled value of the double-sided Fisher exact test on strand balance.
Using default values will have the same behavior as the GATK implementation, that is:
- If sum(counts) > 2*`min_cell_count` (default to GATK value of 200), they are normalized
- If sum(counts) < `min_count` (default to GATK value of 4), returns missing
- Any p-value < `min_p_value` (default to GATK value of 1e-320) is truncated to that value
In addition to the default GATK behavior, setting `normalize` to `False` will perform a chi-squared test
for large counts (> `min_cell_count`) instead of normalizing the cell values.
.. note::
This function can either take
- an array of length four containing the forward and reverse strands' counts of ref and alt alleles: [ref fwd, ref rev, alt fwd, alt rev]
- a two dimensional array with arrays of length two, containing the counts: [[ref fwd, ref rev], [alt fwd, alt rev]]
GATK code here: https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrand.java
:param sb: Count of ref/alt reads on each strand
:param normalize: Whether to normalize counts is sum(counts) > min_cell_count (normalize=True), or use a chi sq instead of FET (normalize=False)
:param min_cell_count: Maximum count for performing a FET
:param min_count: Minimum total count to output FS (otherwise null it output)
:return: FS value
"""
if not isinstance(sb, hl.expr.ArrayNumericExpression):
sb = hl.bind(lambda x: hl.flatten(x), sb)
sb_sum = hl.bind(lambda x: hl.sum(x), sb)
# Normalize table if counts get too large
if normalize:
fs_expr = hl.bind(
lambda sb, sb_sum: hl.cond(
sb_sum <= 2 * min_cell_count,
sb,
sb.map(lambda x: hl.int(x / (sb_sum / min_cell_count))),
),
sb,
sb_sum,
)
# FET
fs_expr = to_phred(
hl.max(
hl.fisher_exact_test(
fs_expr[0], fs_expr[1], fs_expr[2], fs_expr[3]
).p_value,
min_p_value,
)
)
else:
fs_expr = to_phred(
hl.max(
hl.contingency_table_test(
sb[0], sb[1], sb[2], sb[3], min_cell_count=min_cell_count
).p_value,
min_p_value,
)
)
# Return null if counts <= `min_count`
return hl.or_missing(
sb_sum > min_count, hl.max(0, fs_expr) # Needed to avoid -0.0 values
)
def fields_to_array(ds, fields):
return hl.flatten(hl.array([field_to_array(ds, f) for f in fields]))
def fields_to_array(ds, fields):
return hl.flatten(hl.array([field_to_array(ds, f) for f in fields]))
, "TFBS_amplification"
, "TF_binding_site_variant"
, "regulatory_region_ablation"
, "regulatory_region_amplification"
, "feature_elongation"
, "regulatory_region_variant"
, "feature_truncation"
, "intergenic_variant"
]
mt4 = kt2.annotate(transcript_canonicals =kt2.vep.transcript_consequences.filter(lambda tc: tc.canonical == 1))
mt4 = mt4.annotate(
all_transcript_terms = hl.set(hl.flatten(mt4.transcript_canonicals.map(lambda x: x.consequence_terms)))
)
mt4 = mt4.annotate(
Consequence = hl.coalesce( # coalesce means take first non-missing
hl.literal(consequence_in_severity_order).filter(lambda cnsq:
mt4.all_transcript_terms.contains(cnsq)
).head(),
mt4.vep.most_severe_consequence
)
)
mt4 = mt4.annotate(
Gene = hl.if_else(mt4.transcript_canonicals.any(lambda tc: hl.set(tc.consequence_terms).contains(mt4.Consequence)), \
mt4.transcript_canonicals.find(lambda tc: (tc.canonical == 1) & (hl.set(tc.consequence_terms).contains(mt4.Consequence))).gene_symbol, \
mt4.vep.transcript_consequences.find(lambda tc: hl.set(tc.consequence_terms).contains(mt4.Consequence)).gene_symbol), \
