update biotype and consequence enums ids (#825) (#826)

* update ids

* ruff

Author: bpblanken

v03_pipeline/lib/annotations/enums.py

@@ -48,7 +48,6 @@
     'ambiguous_orf',
     'sense_intronic',
     'sense_overlapping',
-    'antisense/antisense_RNA',
     'antisense',
     'known_ncrna',
     'pseudogene',
@@ -64,12 +63,9 @@
     'unprocessed_pseudogene',
     'artifact',
     'lincRNA',
-    'lincrna',
     'macro_lncRNA',
     '3prime_overlapping_ncRNA',
     'disrupted_domain',
-    'vaultRNA/vault_RNA',
-    'vaultRNA',
     'vault_RNA',
     'bidirectional_promoter_lncRNA',
     '3prime_overlapping_ncrna',
@@ -91,9 +87,6 @@
     'frameshift_variant',
     'stop_lost',
     'start_lost',
-    'transcript_amplification',
-    'feature_elongation',
-    'feature_truncation',
     'inframe_insertion',
     'inframe_deletion',
     'missense_variant',

v03_pipeline/lib/annotations/snv_indel_test.py

@@ -132,7 +132,7 @@ def test_sorted_transcript_consequences_37(
                         hgvsp='ENSP00000317992.6:p.Ser556Leu',
                         transcript_id='ENST00000327044',
                         biotype_id=39,
-                        consequence_term_ids=[12],
+                        consequence_term_ids=[9],
                         is_lof_nagnag=None,
                         lof_filter_ids=[0, 1],
                     ),
@@ -145,7 +145,7 @@ def test_sorted_transcript_consequences_37(
                         hgvsp=None,
                         transcript_id='ENST00000477976',
                         biotype_id=38,
-                        consequence_term_ids=[26, 29],
+                        consequence_term_ids=[23, 26],
                         is_lof_nagnag=None,
                         lof_filter_ids=None,
                     ),
@@ -158,7 +158,7 @@ def test_sorted_transcript_consequences_37(
                         hgvsp=None,
                         transcript_id='ENST00000483767',
                         biotype_id=38,
-                        consequence_term_ids=[26, 29],
+                        consequence_term_ids=[23, 26],
                         is_lof_nagnag=None,
                         lof_filter_ids=None,
                     ),
@@ -220,7 +220,7 @@ def test_sorted_transcript_consequences_38(
                     mane_select='NM_015658.4',
                     mane_plus_clinical=None,
                     biotype_id=39,
-                    consequence_term_ids=[12],
+                    consequence_term_ids=[9],
                     exon=hl.Struct(index=15, total=19),
                     intron=None,
                     alphamissense=hl.Struct(pathogenicity=0.10000000149011612),
@@ -251,7 +251,7 @@ def test_sorted_transcript_consequences_38(
                     mane_select=None,
                     mane_plus_clinical=None,
                     biotype_id=38,
-                    consequence_term_ids=[26, 29],
+                    consequence_term_ids=[23, 26],
                     exon=hl.Struct(index=13, total=17),
                     intron=None,
                     alphamissense=hl.Struct(pathogenicity=0.9700000286102295),
@@ -282,7 +282,7 @@ def test_sorted_transcript_consequences_38(
                     mane_select=None,
                     mane_plus_clinical=None,
                     biotype_id=38,
-                    consequence_term_ids=[26, 16, 29],
+                    consequence_term_ids=[23, 13, 26],
                     exon=hl.Struct(index=1, total=5),
                     intron=None,
                     alphamissense=hl.Struct(pathogenicity=None),

v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py

@@ -540,11 +540,11 @@ def test_multiple_update_vat(
                 ht.locus.position <= 878809,  # noqa: PLR2004
             ).sorted_transcript_consequences.consequence_term_ids.collect(),
             [
-                [[12], [26, 29], [26, 16, 29]],
-                [[12], [26, 29], [26, 16, 29]],
-                [[12], [26, 29], [26, 16, 29]],
-                [[12], [26, 29], [26, 16, 29]],
-                [[12], [26, 29], [26, 16, 29]],
+                [[9], [23, 26], [23, 13, 26]],
+                [[9], [23, 26], [23, 13, 26]],
+                [[9], [23, 26], [23, 13, 26]],
+                [[9], [23, 26], [23, 13, 26]],
+                [[9], [23, 26], [23, 13, 26]],
             ],
         )
         self.assertCountEqual(