biotype enums #815
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biotype enums #815
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bpblanken
commented
Jun 21, 2024
| @@ -4,7 +4,7 @@ | |||
| 'IG_C_gene', | |||
| 'IG_D_gene', | |||
| 'IG_J_gene', | |||
| 'IG_LV_gene', | |||
| #'IG_LV_gene', | |||
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Script for this
import hail as hl
ht = hl.read_table('gs://seqr-hail-search-data/v03/GRCh38/SNV_INDEL/annotations.ht')
ht = ht.explode('sorted_transcript_consequences')
biotypes = ht.aggregate(hl.agg.collect_as_set(ht.sorted_transcript_consequences.biotype_id))
missing_38_biotypes = [x for x in range(72) if x not in biotypes]
ht = hl.read_table('gs://seqr-hail-search-data/v03/GRCh37/SNV_INDEL/annotations.ht')
ht = ht.explode('sorted_transcript_consequences')
biotypes = ht.aggregate(hl.agg.collect_as_set(ht.sorted_transcript_consequences.biotype_id))
missing_37_biotypes = [x for x in range(72) if x not in biotypes]
{x for x in set(missing_38_biotypes) if x in set(missing_37_biotypes)}
bpblanken
commented
Jun 24, 2024
| 'vault_RNA', | ||
| 'bidirectional_promoter_lncRNA', | ||
| '3prime_overlapping_ncrna', | ||
| #'3prime_overlapping_ncrna', |
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These are candidates to be removed:
vaultRNA/vault_RNA, vaultRNA, antisense/antisense_RNA, lincrna
|
closing in favor of an actual pr that removes the dupes. |
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