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biotype enums #815

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biotype enums #815

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44 changes: 22 additions & 22 deletions v03_pipeline/lib/annotations/enums.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)}

'IG_V_gene',
'TR_C_gene',
'TR_J_gene',
Expand All @@ -28,14 +28,14 @@
'sRNA',
'scaRNA',
'lncRNA',
'Mt_tRNA_pseudogene',
'tRNA_pseudogene',
'snoRNA_pseudogene',
'snRNA_pseudogene',
'scRNA_pseudogene',
#'Mt_tRNA_pseudogene',
#'tRNA_pseudogene',
#'snoRNA_pseudogene',
#'snRNA_pseudogene',
#'scRNA_pseudogene',
'rRNA_pseudogene',
'misc_RNA_pseudogene',
'miRNA_pseudogene',
#'misc_RNA_pseudogene',
#'miRNA_pseudogene',
'TEC',
'nonsense_mediated_decay',
'non_stop_decay',
Expand All @@ -44,35 +44,35 @@
'protein_coding_LoF',
'protein_coding_CDS_not_defined',
'processed_transcript',
'non_coding',
'ambiguous_orf',
#'non_coding',
#'ambiguous_orf',
'sense_intronic',
'sense_overlapping',
'antisense/antisense_RNA',
#'antisense/antisense_RNA',
'antisense',
'known_ncrna',
#'known_ncrna',
'pseudogene',
'processed_pseudogene',
'polymorphic_pseudogene',
'retrotransposed',
#'retrotransposed',
'transcribed_processed_pseudogene',
'transcribed_unprocessed_pseudogene',
'transcribed_unitary_pseudogene',
'translated_processed_pseudogene',
'translated_unprocessed_pseudogene',
#'translated_unprocessed_pseudogene',
'unitary_pseudogene',
'unprocessed_pseudogene',
'artifact',
#'artifact',
'lincRNA',
'lincrna',
'macro_lncRNA',
'3prime_overlapping_ncRNA',
'disrupted_domain',
'vaultRNA/vault_RNA',
'vaultRNA',
#'lincrna',
#'macro_lncRNA',
#'3prime_overlapping_ncRNA',
#'disrupted_domain',
#'vaultRNA/vault_RNA',
#'vaultRNA',
'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

]

REGULATORY_BIOTYPES = [
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