def create_aggregated_bin_ht(model_id: str) -> hl.Table:
"""
Aggregates variants into bins, grouped by `bin_id` (rank, bi-allelic, etc.), contig, and `snv`, `bi_allelic`,
and `singleton` status, using previously annotated bin information.
For each bin, aggregates statistics needed for evaluation plots.
:param str model_id: Which variant QC model (RF or VQSR model ID) to group
:return: Table of aggregate statistics by bin
"""
ht = get_score_bins(model_id, aggregated=False).ht()
# Count variants for ranking
count_expr = {
x: hl.agg.filter(
hl.is_defined(ht[x]),
hl.agg.counter(
hl.cond(hl.is_snp(ht.alleles[0], ht.alleles[1]), "snv",
"indel")),
)
for x in ht.row if x.endswith("bin")
}
bin_variant_counts = ht.aggregate(hl.struct(**count_expr))
logger.info(
f"Found the following variant counts:\n {pformat(bin_variant_counts)}")
ht = ht.annotate_globals(bin_variant_counts=bin_variant_counts)
# Load ClinVar pathogenic data
clinvar_pathogenic_ht = filter_to_clinvar_pathogenic(clinvar.ht())
ht = ht.annotate(clinvar_path=hl.is_defined(clinvar_pathogenic_ht[ht.key]))
trio_stats_ht = fam_stats.ht()
logger.info(f"Creating grouped bin table...")
grouped_binned_ht = compute_grouped_binned_ht(
ht,
checkpoint_path=get_checkpoint_path(f"grouped_bin_{model_id}"),
)
logger.info(f"Aggregating grouped bin table...")
parent_ht = grouped_binned_ht._parent
agg_ht = grouped_binned_ht.aggregate(
n_clinvar_path=hl.agg.count_where(parent_ht.clinvar_path),
**score_bin_agg(grouped_binned_ht, fam_stats_ht=trio_stats_ht),
)
return agg_ht
def create_grouped_bin_ht(model_id: str, overwrite: bool = False) -> None:
"""
Creates binned data from a quantile bin annotated Table grouped by bin_id (rank, bi-allelic, etc.), contig, snv,
bi_allelic and singleton containing the information needed for evaluation plots.
:param str model_id: Which data/run hash is being created
:param bool overwrite: Should output files be overwritten if present
:return: None
:rtype: None
"""
ht = get_score_quantile_bins(model_id, aggregated=False).ht()
# Count variants for ranking
count_expr = {
x: hl.agg.filter(
hl.is_defined(ht[x]),
hl.agg.counter(
hl.cond(hl.is_snp(ht.alleles[0], ht.alleles[1]), "snv",
"indel")),
)
for x in ht.row if x.endswith("bin")
}
bin_variant_counts = ht.aggregate(hl.struct(**count_expr))
logger.info(
f"Found the following variant counts:\n {pformat(bin_variant_counts)}")
ht = ht.annotate_globals(bin_variant_counts=bin_variant_counts)
trio_stats_ht = fam_stats.ht()
logger.info(f"Creating grouped bin table...")
grouped_binned_ht = compute_grouped_binned_ht(
ht,
checkpoint_path=get_checkpoint_path(f"grouped_bin_{model_id}"),
)
logger.info(f"Aggregating grouped bin table...")
agg_ht = grouped_binned_ht.aggregate(
**score_bin_agg(grouped_binned_ht, fam_stats_ht=trio_stats_ht))
agg_ht.write(
get_score_quantile_bins(model_id, aggregated=True).path,
overwrite=overwrite,
)
