Skip to content

Commit

Permalink
Update v2 rmc task for public data (#1332)
Browse files Browse the repository at this point in the history
  • Loading branch information
rileyhgrant authored Dec 1, 2023
1 parent 55adbc1 commit bab4837
Showing 1 changed file with 2 additions and 8 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -29,13 +29,7 @@ def prepare_gnomad_v2_regional_missense_constraint(path):

ds_with_rmc = ds_with_rmc.group_by("transcript_id").aggregate(regions_array=hl.agg.collect(ds_with_rmc.row_value))
ds_with_rmc = ds_with_rmc.annotate(has_no_rmc_evidence=hl.bool(False))
ds_with_rmc = ds_with_rmc.annotate(
passed_qc=hl.if_else(
hl.set(ds_with_rmc.globals.rmc_transcripts_qc).contains(ds_with_rmc.transcript_id),
hl.bool(True),
hl.bool(False),
)
)
ds_with_rmc = ds_with_rmc.annotate(passed_qc=hl.bool(True))
ds_with_rmc = ds_with_rmc.select(
has_no_rmc_evidence=ds_with_rmc.has_no_rmc_evidence,
passed_qc=ds_with_rmc.passed_qc,
Expand All @@ -46,7 +40,7 @@ def prepare_gnomad_v2_regional_missense_constraint(path):
# the browser needs to be able to distinguish between transcripts that were
# searched and had no RMC evidence, vs those that were not searched, for display
# purposes
no_rmc_set = ds.globals.transcripts_no_rmc_all
no_rmc_set = ds.globals.transcripts_no_rmc
no_rmc_list = list(no_rmc_set.collect()[0])
ds_no_rmc = hl.utils.range_table(1)
ds_no_rmc = ds_no_rmc.annotate(
Expand Down

0 comments on commit bab4837

Please sign in to comment.