def liftover_using_gnomad_map(ht, data_type):
"""
Liftover a gnomAD table using already-established liftover file. Warning: shuffles!
:param ht: Input Hail table
:param data_type: one of "exomes" or "genomes" which to map across
:return: Lifted over table
"""
from gnomad.resources.grch37.gnomad import liftover
lift_ht = liftover(data_type).ht()
ht = ht.key_by(original_locus=ht.locus,
original_alleles=ht.alleles).drop('locus', 'alleles')
return lift_ht.annotate(**ht[(lift_ht.original_locus,
lift_ht.original_alleles)]).key_by(
'locus', 'alleles')
def liftover_using_gnomad_map(ht: hl.Table, data_type: str):
"""
Liftover a gnomAD v2 table using already-established liftover file.
.. note::
This function shuffles!
:param ht: Input Hail Table.
:param data_type: Which gnomAD data type to map across. One of "exomes" or "genomes".
:return: Lifted over Table
"""
from gnomad.resources.grch37.gnomad import liftover
logger.warning(
"This function will trigger a shuffle! Pre-emptibles may not work.")
lift_ht = liftover(data_type).ht()
ht = ht.key_by(original_locus=ht.locus,
original_alleles=ht.alleles).drop("locus", "alleles")
return lift_ht.annotate(**ht[(lift_ht.original_locus,
lift_ht.original_alleles)]).key_by(
"locus", "alleles")