diff --git a/backend/Makefile b/backend/Makefile index cfd23f258..be89da0b5 100644 --- a/backend/Makefile +++ b/backend/Makefile @@ -154,7 +154,7 @@ gen-api-schema: .PHONY: protos-build protos-build: PYTHONPATH=. \ - protoc \ + pipenv run python -m grpc_tools.protoc \ -Iprotos \ --python_out=. \ --mypy_out=. \ diff --git a/backend/Pipfile b/backend/Pipfile index 2464e220c..989427fab 100644 --- a/backend/Pipfile +++ b/backend/Pipfile @@ -80,7 +80,6 @@ flake8-pyproject = "*" freezegun = "~=1.5" isort = "~=7.0" jsonmatch = "*" -mypy-protobuf = "*" openpyxl = "~=3.1" parameterized = "~=0.9.0" protolint-bin = "*" @@ -96,6 +95,8 @@ watchdog = "*" werkzeug = "~=3.1.6" uritemplate = "*" django-types = "*" +grpcio-tools = "==1.68.1" +mypy-protobuf = "==3.6.0" [ldap-packages] # Dependencies for enabling LDAP support. You will need the system library diff --git a/backend/Pipfile.lock b/backend/Pipfile.lock index 3c393bae3..5177cc0b5 100644 --- a/backend/Pipfile.lock +++ b/backend/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "675a8fd71d249fa7513a36933ee10acee31fdcdc80d17b0174fcef97ce7eef31" + "sha256": "0a2fe00aacfd368279fd6372dedf7d5e542f5aa8a112df01e851c4b9b878df12" }, "pipfile-spec": 6, "requires": { @@ -4120,6 +4120,135 @@ "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'", "version": "==1.0.0" }, + "grpcio": { + "hashes": [ + "sha256:00168469238b022500e486c1c33916acf2f2a9b2c022202cf8a1885d2e3073c1", + "sha256:02e64bb0bb2da14d947a49e6f120a75e947250aebe65f9629b62bb1f5c14e6e9", + "sha256:05d55e1798756282cddd52d56c896b3e7d673e3a8798c2f1cd05ba249a3bb4de", + "sha256:09e5e478b3d14afd23f12e49e8b44c8684ac3c5f08561c43a5b9691c54d136ab", + "sha256:0cb517eb1d0d0aaf1d87af7cc5b801d686557c1d88b2619f5e31fab3c2315921", + 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"sha256:8493758852a9cdc075a11dbe96c6e37ea2feba5fd5f33ef7442b9a275322a94c", - "sha256:d7031f563f806b8bcd448a3e86768bf0994c0af5b0017b344a4fbbba4191f43c" + "sha256:02f242eb3409f66889f2b1a3aa58356ec4d909cdd0f93115622e9e70366eca3c", + "sha256:56176e4d569070e7350ea620262478b49b7efceba4103d468448f1d21492fd6c" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==5.1.0" + "version": "==3.6.0" }, "openpyxl": { "hashes": [ @@ -4711,12 +4840,12 @@ }, "types-protobuf": { "hashes": [ - "sha256:75fd66121d56785c91828b8bf7b511f39ba847f11e682573e41847f01e9cd1de", - "sha256:effbc819aa17e02448dde99f089c6794662d66f4b2797e922f185ffe0b24e766" + "sha256:1c93e8c294281b76a5255fc21c747db0004694463ac6ea9866ee06da969fa555", + "sha256:a5d647381f8651bd505304ed1148b8a7b342781796e0f80e0284c774c2262a09" ], "index": "pypi", "markers": "python_version >= '3.10'", - "version": "==7.34.1.20260503" + "version": "==7.34.1.20260508" }, "types-psycopg2": { "hashes": [ diff --git a/backend/protos/seqvars/protos/query.proto b/backend/protos/seqvars/protos/query.proto index 175e34a54..073f49774 100644 --- a/backend/protos/seqvars/protos/query.proto +++ b/backend/protos/seqvars/protos/query.proto @@ -216,6 +216,14 @@ enum Consequence { CONSEQUENCE_RARE_AMINO_ACID_VARIANT = 45; // Protein altering variant CONSEQUENCE_PROTEIN_ALTERING_VARIANT = 46; + // Inframe deletion + CONSEQUENCE_INFRAME_DELETION = 49; + // Inframe insertion + CONSEQUENCE_INFRAME_INSERTION = 50; + // Selenocysteine gain + CONSEQUENCE_SELENOCYSTEINE_GAIN = 51; + // Selenocysteine loss + CONSEQUENCE_SELENOCYSTEINE_LOSS = 52; /* * low impact */ @@ -235,6 +243,8 @@ enum Consequence { CONSEQUENCE_STOP_RETAINED_VARIANT = 22; // Synonymous variant. CONSEQUENCE_SYNONYMOUS_VARIANT = 23; + // Incomplete terminal codon variant + CONSEQUENCE_INCOMPLETE_TERMINAL_CODON_VARIANT = 53; /* * modifier */ @@ -246,14 +256,20 @@ enum Consequence { CONSEQUENCE_FIVE_PRIME_UTR_EXON_VARIANT = 26; // 5' UTR intron variant. CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT = 27; + // 5' UTR variant. + CONSEQUENCE_FIVE_PRIME_UTR_VARIANT = 54; // 3' UTR exon variant. CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT = 28; // 3' UTR intron variant. CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT = 29; + // 3' UTR variant. + CONSEQUENCE_THREE_PRIME_UTR_VARIANT = 55; // Non-coding transcript exon variant. CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT = 30; // Non-coding transcript intron variant. CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT = 31; + // Non-coding transcript variant. + CONSEQUENCE_NON_CODING_TRANSCRIPT_VARIANT = 56; // Coding transcript intron variant. CONSEQUENCE_CODING_TRANSCRIPT_INTRON_VARIANT = 48; // Upstream gene variant. diff --git a/backend/seqvars/factory_defaults.py b/backend/seqvars/factory_defaults.py index 20f79cc8d..77a10f832 100644 --- a/backend/seqvars/factory_defaults.py +++ b/backend/seqvars/factory_defaults.py @@ -139,6 +139,10 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres SeqvarsVariantConsequenceChoice.MISSENSE_VARIANT, SeqvarsVariantConsequenceChoice.RARE_AMINO_ACID_VARIANT, SeqvarsVariantConsequenceChoice.PROTEIN_ALTERING_VARIANT, + SeqvarsVariantConsequenceChoice.INFRAME_DELETION, + SeqvarsVariantConsequenceChoice.INFRAME_INSERTION, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_GAIN, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_LOSS, # low impact SeqvarsVariantConsequenceChoice.SPLICE_DONOR_FIFTH_BASE_VARIANT, SeqvarsVariantConsequenceChoice.SPLICE_REGION_VARIANT, @@ -148,15 +152,19 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres SeqvarsVariantConsequenceChoice.START_RETAINED_VARIANT, SeqvarsVariantConsequenceChoice.STOP_RETAINED_VARIANT, SeqvarsVariantConsequenceChoice.SYNONYMOUS_VARIANT, + SeqvarsVariantConsequenceChoice.INCOMPLETE_TERMINAL_CODON_VARIANT, # modifier SeqvarsVariantConsequenceChoice.CODING_SEQUENCE_VARIANT, # SeqvarsVariantConsequenceChoice.MATURE_MIRNA_VARIANT, SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_EXON_VARIANT, SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_VARIANT, SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_EXON_VARIANT, SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_VARIANT, SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_EXON_VARIANT, SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_VARIANT, SeqvarsVariantConsequenceChoice.CODING_TRANSCRIPT_INTRON_VARIANT, SeqvarsVariantConsequenceChoice.UPSTREAM_GENE_VARIANT, SeqvarsVariantConsequenceChoice.DOWNSTREAM_GENE_VARIANT, @@ -210,6 +218,10 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres # SeqvarsVariantConsequenceChoice.MISSENSE_VARIANT, # SeqvarsVariantConsequenceChoice.RARE_AMINO_ACID_VARIANT, # SeqvarsVariantConsequenceChoice.PROTEIN_ALTERING_VARIANT, + # SeqvarsVariantConsequenceChoice.INFRAME_DELETION, + # SeqvarsVariantConsequenceChoice.INFRAME_INSERTION, + # SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_GAIN, + # SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_LOSS, # # low impact # SeqvarsVariantConsequenceChoice.SPLICE_DONOR_FIFTH_BASE_VARIANT, # SeqvarsVariantConsequenceChoice.SPLICE_REGION_VARIANT, @@ -219,15 +231,19 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres # SeqvarsVariantConsequenceChoice.START_RETAINED_VARIANT, # SeqvarsVariantConsequenceChoice.STOP_RETAINED_VARIANT, # SeqvarsVariantConsequenceChoice.SYNONYMOUS_VARIANT, + # SeqvarsVariantConsequenceChoice.INCOMPLETE_TERMINAL_CODON_VARIANT, # # modifier # SeqvarsVariantConsequenceChoice.CODING_SEQUENCE_VARIANT, # SeqvarsVariantConsequenceChoice.MATURE_MIRNA_VARIANT, # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_VARIANT, # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_VARIANT, # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_VARIANT, # SeqvarsVariantConsequenceChoice.CODING_TRANSCRIPT_INTRON_VARIANT, # SeqvarsVariantConsequenceChoice.UPSTREAM_GENE_VARIANT, # SeqvarsVariantConsequenceChoice.DOWNSTREAM_GENE_VARIANT, @@ -281,6 +297,10 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres SeqvarsVariantConsequenceChoice.MISSENSE_VARIANT, SeqvarsVariantConsequenceChoice.RARE_AMINO_ACID_VARIANT, SeqvarsVariantConsequenceChoice.PROTEIN_ALTERING_VARIANT, + SeqvarsVariantConsequenceChoice.INFRAME_DELETION, + SeqvarsVariantConsequenceChoice.INFRAME_INSERTION, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_GAIN, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_LOSS, # low impact SeqvarsVariantConsequenceChoice.SPLICE_DONOR_FIFTH_BASE_VARIANT, SeqvarsVariantConsequenceChoice.SPLICE_REGION_VARIANT, @@ -290,15 +310,19 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres # SeqvarsVariantConsequenceChoice.START_RETAINED_VARIANT, # SeqvarsVariantConsequenceChoice.STOP_RETAINED_VARIANT, # SeqvarsVariantConsequenceChoice.SYNONYMOUS_VARIANT, + SeqvarsVariantConsequenceChoice.INCOMPLETE_TERMINAL_CODON_VARIANT, # # modifier # SeqvarsVariantConsequenceChoice.CODING_SEQUENCE_VARIANT, # SeqvarsVariantConsequenceChoice.MATURE_MIRNA_VARIANT, # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_VARIANT, # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_VARIANT, # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_VARIANT, # SeqvarsVariantConsequenceChoice.CODING_TRANSCRIPT_INTRON_VARIANT, # SeqvarsVariantConsequenceChoice.UPSTREAM_GENE_VARIANT, # SeqvarsVariantConsequenceChoice.DOWNSTREAM_GENE_VARIANT, @@ -353,6 +377,10 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres SeqvarsVariantConsequenceChoice.MISSENSE_VARIANT, SeqvarsVariantConsequenceChoice.RARE_AMINO_ACID_VARIANT, SeqvarsVariantConsequenceChoice.PROTEIN_ALTERING_VARIANT, + SeqvarsVariantConsequenceChoice.INFRAME_DELETION, + SeqvarsVariantConsequenceChoice.INFRAME_INSERTION, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_GAIN, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_LOSS, # low impact SeqvarsVariantConsequenceChoice.SPLICE_DONOR_FIFTH_BASE_VARIANT, SeqvarsVariantConsequenceChoice.SPLICE_REGION_VARIANT, @@ -362,15 +390,19 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres SeqvarsVariantConsequenceChoice.START_RETAINED_VARIANT, SeqvarsVariantConsequenceChoice.STOP_RETAINED_VARIANT, SeqvarsVariantConsequenceChoice.SYNONYMOUS_VARIANT, + SeqvarsVariantConsequenceChoice.INCOMPLETE_TERMINAL_CODON_VARIANT, # # modifier SeqvarsVariantConsequenceChoice.CODING_SEQUENCE_VARIANT, # SeqvarsVariantConsequenceChoice.MATURE_MIRNA_VARIANT, # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_VARIANT, # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_VARIANT, # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_EXON_VARIANT, # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_INTRON_VARIANT, + # SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_VARIANT, SeqvarsVariantConsequenceChoice.CODING_TRANSCRIPT_INTRON_VARIANT, # SeqvarsVariantConsequenceChoice.UPSTREAM_GENE_VARIANT, # SeqvarsVariantConsequenceChoice.DOWNSTREAM_GENE_VARIANT, @@ -425,6 +457,10 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres SeqvarsVariantConsequenceChoice.MISSENSE_VARIANT, SeqvarsVariantConsequenceChoice.RARE_AMINO_ACID_VARIANT, SeqvarsVariantConsequenceChoice.PROTEIN_ALTERING_VARIANT, + SeqvarsVariantConsequenceChoice.INFRAME_DELETION, + SeqvarsVariantConsequenceChoice.INFRAME_INSERTION, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_GAIN, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_LOSS, # low impact SeqvarsVariantConsequenceChoice.SPLICE_DONOR_FIFTH_BASE_VARIANT, SeqvarsVariantConsequenceChoice.SPLICE_REGION_VARIANT, @@ -434,15 +470,19 @@ def create_seqvarsquerypresetsconsequence(faker: Faker) -> list[SeqvarsQueryPres SeqvarsVariantConsequenceChoice.START_RETAINED_VARIANT, SeqvarsVariantConsequenceChoice.STOP_RETAINED_VARIANT, SeqvarsVariantConsequenceChoice.SYNONYMOUS_VARIANT, + SeqvarsVariantConsequenceChoice.INCOMPLETE_TERMINAL_CODON_VARIANT, # modifier SeqvarsVariantConsequenceChoice.CODING_SEQUENCE_VARIANT, # SeqvarsVariantConsequenceChoice.MATURE_MIRNA_VARIANT, SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_EXON_VARIANT, SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_VARIANT, SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_EXON_VARIANT, SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_VARIANT, SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_EXON_VARIANT, SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_VARIANT, SeqvarsVariantConsequenceChoice.CODING_TRANSCRIPT_INTRON_VARIANT, SeqvarsVariantConsequenceChoice.UPSTREAM_GENE_VARIANT, SeqvarsVariantConsequenceChoice.DOWNSTREAM_GENE_VARIANT, diff --git a/backend/seqvars/models/base.py b/backend/seqvars/models/base.py index 2ebbb0038..27e05ffb1 100644 --- a/backend/seqvars/models/base.py +++ b/backend/seqvars/models/base.py @@ -206,6 +206,10 @@ class SeqvarsVariantConsequenceChoice(str, Enum): # moderate impact + #: Inframe insertion + INFRAME_INSERTION = "inframe_insertion" + #: Inframe deletion + INFRAME_DELETION = "inframe_deletion" #: Disruptive inframe insertion DISRUPTIVE_INFRAME_INSERTION = "disruptive_inframe_insertion" #: Disruptive inframe deletion @@ -220,9 +224,15 @@ class SeqvarsVariantConsequenceChoice(str, Enum): RARE_AMINO_ACID_VARIANT = "rare_amino_acid_variant" #: Protein altering variant PROTEIN_ALTERING_VARIANT = "protein_altering_variant" + #: Selenocysteine gain + SELENOCYSTEINE_GAIN = "selenocysteine_gain" + #: Selenocysteine loss + SELENOCYSTEINE_LOSS = "selenocysteine_loss" # low impact + #: Incomplete terminal codon variant. + INCOMPLETE_TERMINAL_CODON_VARIANT = "incomplete_terminal_codon_variant" #: Splice donor 5th base variant. SPLICE_DONOR_FIFTH_BASE_VARIANT = "splice_donor_5th_base_variant" #: Splice region variant. @@ -250,14 +260,20 @@ class SeqvarsVariantConsequenceChoice(str, Enum): FIVE_PRIME_UTR_EXON_VARIANT = "5_prime_UTR_exon_variant" #: 5' UTR intron variant. FIVE_PRIME_UTR_INTRON_VARIANT = "5_prime_UTR_intron_variant" + #: 5' UTR variant. + FIVE_PRIME_UTR_VARIANT = "5_prime_UTR_variant" #: 3' UTR exon variant. THREE_PRIME_UTR_EXON_VARIANT = "3_prime_UTR_exon_variant" #: 3' UTR intron variant. THREE_PRIME_UTR_INTRON_VARIANT = "3_prime_UTR_intron_variant" + #: 3' UTR variant. + THREE_PRIME_UTR_VARIANT = "3_prime_UTR_variant" #: Non-coding transcript exon variant. NON_CODING_TRANSCRIPT_EXON_VARIANT = "non_coding_transcript_exon_variant" #: Non-coding transcript intron variant. NON_CODING_TRANSCRIPT_INTRON_VARIANT = "non_coding_transcript_intron_variant" + #: Non-coding transcript variant. + NON_CODING_TRANSCRIPT_VARIANT = "non_coding_transcript_variant" #: Coding transcript intron variant. CODING_TRANSCRIPT_INTRON_VARIANT = "coding_transcript_intron_variant" #: Upstream gene variant. diff --git a/backend/seqvars/models/protobufs.py b/backend/seqvars/models/protobufs.py index f6cf75043..eb3c91b02 100644 --- a/backend/seqvars/models/protobufs.py +++ b/backend/seqvars/models/protobufs.py @@ -264,6 +264,11 @@ def _frequency_to_protobuf(frequency: SeqvarsQuerySettingsFrequency) -> QuerySet SeqvarsVariantConsequenceChoice.MISSENSE_VARIANT: Consequence.CONSEQUENCE_MISSENSE_VARIANT, SeqvarsVariantConsequenceChoice.RARE_AMINO_ACID_VARIANT: Consequence.CONSEQUENCE_RARE_AMINO_ACID_VARIANT, SeqvarsVariantConsequenceChoice.PROTEIN_ALTERING_VARIANT: Consequence.CONSEQUENCE_PROTEIN_ALTERING_VARIANT, + SeqvarsVariantConsequenceChoice.INFRAME_DELETION: Consequence.CONSEQUENCE_INFRAME_DELETION, + SeqvarsVariantConsequenceChoice.INFRAME_INSERTION: Consequence.CONSEQUENCE_INFRAME_INSERTION, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_GAIN: Consequence.CONSEQUENCE_SELENOCYSTEINE_GAIN, + SeqvarsVariantConsequenceChoice.SELENOCYSTEINE_LOSS: Consequence.CONSEQUENCE_SELENOCYSTEINE_LOSS, + SeqvarsVariantConsequenceChoice.INCOMPLETE_TERMINAL_CODON_VARIANT: Consequence.CONSEQUENCE_INCOMPLETE_TERMINAL_CODON_VARIANT, SeqvarsVariantConsequenceChoice.SPLICE_DONOR_FIFTH_BASE_VARIANT: Consequence.CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT, SeqvarsVariantConsequenceChoice.SPLICE_REGION_VARIANT: Consequence.CONSEQUENCE_SPLICE_REGION_VARIANT, SeqvarsVariantConsequenceChoice.EXONIC_SPLICE_REGION_VARIANT: Consequence.CONSEQUENCE_EXONIC_SPLICE_REGION_VARIANT, @@ -276,10 +281,13 @@ def _frequency_to_protobuf(frequency: SeqvarsQuerySettingsFrequency) -> QuerySet SeqvarsVariantConsequenceChoice.MATURE_MIRNA_VARIANT: Consequence.CONSEQUENCE_MATURE_MIRNA_VARIANT, SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_EXON_VARIANT: Consequence.CONSEQUENCE_FIVE_PRIME_UTR_EXON_VARIANT, SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_INTRON_VARIANT: Consequence.CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.FIVE_PRIME_UTR_VARIANT: Consequence.CONSEQUENCE_FIVE_PRIME_UTR_VARIANT, SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_EXON_VARIANT: Consequence.CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT, SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_INTRON_VARIANT: Consequence.CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.THREE_PRIME_UTR_VARIANT: Consequence.CONSEQUENCE_THREE_PRIME_UTR_VARIANT, SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_EXON_VARIANT: Consequence.CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT, SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_INTRON_VARIANT: Consequence.CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT, + SeqvarsVariantConsequenceChoice.NON_CODING_TRANSCRIPT_VARIANT: Consequence.CONSEQUENCE_NON_CODING_TRANSCRIPT_VARIANT, SeqvarsVariantConsequenceChoice.CODING_TRANSCRIPT_INTRON_VARIANT: Consequence.CONSEQUENCE_CODING_TRANSCRIPT_INTRON_VARIANT, SeqvarsVariantConsequenceChoice.UPSTREAM_GENE_VARIANT: Consequence.CONSEQUENCE_UPSTREAM_GENE_VARIANT, SeqvarsVariantConsequenceChoice.DOWNSTREAM_GENE_VARIANT: Consequence.CONSEQUENCE_DOWNSTREAM_GENE_VARIANT, diff --git a/backend/seqvars/protos/output_pb2.py b/backend/seqvars/protos/output_pb2.py index 0fa0c8096..ef6742889 100644 --- a/backend/seqvars/protos/output_pb2.py +++ b/backend/seqvars/protos/output_pb2.py @@ -1,12 +1,18 @@ # -*- coding: utf-8 -*- # Generated by the protocol buffer compiler. DO NOT EDIT! +# NO CHECKED-IN PROTOBUF GENCODE # source: seqvars/protos/output.proto +# Protobuf Python Version: 5.28.1 """Generated protocol buffer code.""" from google.protobuf import descriptor as _descriptor from google.protobuf import descriptor_pool as _descriptor_pool +from google.protobuf import runtime_version as _runtime_version from google.protobuf import symbol_database as _symbol_database from google.protobuf.internal import builder as _builder +_runtime_version.ValidateProtobufRuntimeVersion( + _runtime_version.Domain.PUBLIC, 5, 28, 1, "", "seqvars/protos/output.proto" +) # @@protoc_insertion_point(imports) _sym_db = _symbol_database.Default() @@ -21,81 +27,81 @@ b'\n\x1bseqvars/protos/output.proto\x12\x12seqvars.pbs.output\x1a\x1cgoogle/protobuf/struct.proto\x1a\x1fgoogle/protobuf/timestamp.proto\x1a\x1aseqvars/protos/query.proto"\xaa\x03\n\x0cOutputHeader\x12\x39\n\x0egenome_release\x18\x01 \x01(\x0e\x32!.seqvars.pbs.output.GenomeRelease\x12\x32\n\x08versions\x18\x02 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b/backend/seqvars/protos/output_pb2.pyi index 27c510b94..69197c6db 100644 --- a/backend/seqvars/protos/output_pb2.pyi +++ b/backend/seqvars/protos/output_pb2.pyi @@ -29,7 +29,7 @@ class _VariantScoreColumnType: class _VariantScoreColumnTypeEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_VariantScoreColumnType.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor VARIANT_SCORE_COLUMN_TYPE_UNSPECIFIED: _VariantScoreColumnType.ValueType # 0 """Unspecified variant score type.""" @@ -58,7 +58,7 @@ class _GenomeRelease: class _GenomeReleaseEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_GenomeRelease.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor GENOME_RELEASE_UNSPECIFIED: _GenomeRelease.ValueType # 0 """Unspecified genome release.""" @@ -85,7 +85,7 @@ class _TranscriptType: class _TranscriptTypeEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_TranscriptType.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor TRANSCRIPT_TYPE_UNSPECIFIED: _TranscriptType.ValueType # 0 """Unknown transcript type.""" @@ -112,7 +112,7 @@ class _VariantLocation: class _VariantLocationEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_VariantLocation.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor VARIANT_LOCATION_UNSPECIFIED: _VariantLocation.ValueType # 0 """Unspecified location.""" @@ -147,7 +147,7 @@ class _ModeOfInheritance: class _ModeOfInheritanceEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_ModeOfInheritance.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor MODE_OF_INHERITANCE_UNSPECIFIED: _ModeOfInheritance.ValueType # 0 """Unspecified mode of inheritance.""" @@ -190,7 +190,7 @@ class _ClingenDosageScore: class _ClingenDosageScoreEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_ClingenDosageScore.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor CLINGEN_DOSAGE_SCORE_UNSPECIFIED: _ClingenDosageScore.ValueType # 0 """Unspecified""" @@ -235,7 +235,7 @@ class _AggregateGermlineReviewStatusEnumTypeWrapper( _AggregateGermlineReviewStatus.ValueType ], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor AGGREGATE_GERMLINE_REVIEW_STATUS_UNSPECIFIED: _AggregateGermlineReviewStatus.ValueType # 0 """unspecified aggregate germline review status value""" @@ -319,6 +319,7 @@ AGGREGATE_GERMLINE_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT: ( """corresponds to "no classification for the single variant" """ global___AggregateGermlineReviewStatus = AggregateGermlineReviewStatus +@typing.final class OutputHeader(google.protobuf.message.Message): """Store meta information about query results.""" @@ -333,6 +334,8 @@ class OutputHeader(google.protobuf.message.Message): VARIANT_SCORE_COLUMNS_FIELD_NUMBER: builtins.int genome_release: global___GenomeRelease.ValueType """Genome release.""" + case_uuid: builtins.str + """Case UUID.""" @property def versions( self, @@ -342,8 +345,7 @@ class OutputHeader(google.protobuf.message.Message): @property def query(self) -> seqvars.protos.query_pb2.CaseQuery: """The used query settings.""" - case_uuid: builtins.str - """Case UUID.""" + @property def resources(self) -> global___ResourcesUsed: """Resources used.""" @@ -373,7 +375,7 @@ class OutputHeader(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_query", b"_query", "_resources", @@ -390,7 +392,7 @@ class OutputHeader(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_query", b"_query", "_resources", @@ -415,19 +417,20 @@ class OutputHeader(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_query", b"_query"] - ) -> typing_extensions.Literal["query"] | None: ... + self, oneof_group: typing.Literal["_query", b"_query"] + ) -> typing.Literal["query"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_resources", b"_resources"] - ) -> typing_extensions.Literal["resources"] | None: ... + self, oneof_group: typing.Literal["_resources", b"_resources"] + ) -> typing.Literal["resources"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_statistics", b"_statistics"] - ) -> typing_extensions.Literal["statistics"] | None: ... + self, oneof_group: typing.Literal["_statistics", b"_statistics"] + ) -> typing.Literal["statistics"] | None: ... global___OutputHeader = OutputHeader +@typing.final class VariantScoreColumn(google.protobuf.message.Message): """Store information about the variant scores in the output.""" @@ -455,13 +458,14 @@ class VariantScoreColumn(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "description", b"description", "label", b"label", "name", b"name", "type", b"type" ], ) -> None: ... global___VariantScoreColumn = VariantScoreColumn +@typing.final class VersionEntry(google.protobuf.message.Message): """Store version information.""" @@ -480,11 +484,12 @@ class VersionEntry(google.protobuf.message.Message): version: builtins.str = ..., ) -> None: ... def ClearField( - self, field_name: typing_extensions.Literal["name", b"name", "version", b"version"] + self, field_name: typing.Literal["name", b"name", "version", b"version"] ) -> None: ... global___VersionEntry = VersionEntry +@typing.final class ResourcesUsed(google.protobuf.message.Message): """Query resource requirements.""" @@ -493,6 +498,8 @@ class ResourcesUsed(google.protobuf.message.Message): START_TIME_FIELD_NUMBER: builtins.int END_TIME_FIELD_NUMBER: builtins.int MEMORY_USED_FIELD_NUMBER: builtins.int + memory_used: builtins.int + """RAM usage in bytes.""" @property def start_time(self) -> google.protobuf.timestamp_pb2.Timestamp: """Start time.""" @@ -500,8 +507,7 @@ class ResourcesUsed(google.protobuf.message.Message): @property def end_time(self) -> google.protobuf.timestamp_pb2.Timestamp: """End time.""" - memory_used: builtins.int - """RAM usage in bytes.""" + def __init__( self, *, @@ -511,7 +517,7 @@ class ResourcesUsed(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_end_time", b"_end_time", "_start_time", @@ -524,7 +530,7 @@ class ResourcesUsed(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_end_time", b"_end_time", "_start_time", @@ -539,15 +545,16 @@ class ResourcesUsed(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_end_time", b"_end_time"] - ) -> typing_extensions.Literal["end_time"] | None: ... + self, oneof_group: typing.Literal["_end_time", b"_end_time"] + ) -> typing.Literal["end_time"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_start_time", b"_start_time"] - ) -> typing_extensions.Literal["start_time"] | None: ... + self, oneof_group: typing.Literal["_start_time", b"_start_time"] + ) -> typing.Literal["start_time"] | None: ... global___ResourcesUsed = ResourcesUsed +@typing.final class OutputStatistics(google.protobuf.message.Message): """Store statistics about the output.""" @@ -577,7 +584,7 @@ class OutputStatistics(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "count_passed", b"count_passed", "count_total", @@ -589,6 +596,7 @@ class OutputStatistics(google.protobuf.message.Message): global___OutputStatistics = OutputStatistics +@typing.final class ConsequenceCount(google.protobuf.message.Message): """Store consequence statistics.""" @@ -607,12 +615,12 @@ class ConsequenceCount(google.protobuf.message.Message): count: builtins.int = ..., ) -> None: ... def ClearField( - self, - field_name: typing_extensions.Literal["consequence", b"consequence", "count", b"count"], + self, field_name: typing.Literal["consequence", b"consequence", "count", b"count"] ) -> None: ... global___ConsequenceCount = ConsequenceCount +@typing.final class OutputRecord(google.protobuf.message.Message): """Store one record in the output.""" @@ -644,7 +652,7 @@ class OutputRecord(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_variant_annotation", b"_variant_annotation", "_vcf_variant", @@ -657,7 +665,7 @@ class OutputRecord(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_variant_annotation", b"_variant_annotation", "_vcf_variant", @@ -674,15 +682,16 @@ class OutputRecord(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_variant_annotation", b"_variant_annotation"] - ) -> typing_extensions.Literal["variant_annotation"] | None: ... + self, oneof_group: typing.Literal["_variant_annotation", b"_variant_annotation"] + ) -> typing.Literal["variant_annotation"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_vcf_variant", b"_vcf_variant"] - ) -> typing_extensions.Literal["vcf_variant"] | None: ... + self, oneof_group: typing.Literal["_vcf_variant", b"_vcf_variant"] + ) -> typing.Literal["vcf_variant"] | None: ... global___OutputRecord = OutputRecord +@typing.final class VcfVariant(google.protobuf.message.Message): """Store a sequnce variant in VCF representation.""" @@ -718,7 +727,7 @@ class VcfVariant(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "alt_allele", b"alt_allele", "chrom", @@ -736,6 +745,7 @@ class VcfVariant(google.protobuf.message.Message): global___VcfVariant = VcfVariant +@typing.final class VariantAnnotation(google.protobuf.message.Message): """Store the variant annotation payload (always for a single gene).""" @@ -765,7 +775,7 @@ class VariantAnnotation(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_call", b"_call", "_gene", @@ -782,7 +792,7 @@ class VariantAnnotation(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_call", b"_call", "_gene", @@ -799,19 +809,20 @@ class VariantAnnotation(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_call", b"_call"] - ) -> typing_extensions.Literal["call"] | None: ... + self, oneof_group: typing.Literal["_call", b"_call"] + ) -> typing.Literal["call"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_gene", b"_gene"] - ) -> typing_extensions.Literal["gene"] | None: ... + self, oneof_group: typing.Literal["_gene", b"_gene"] + ) -> typing.Literal["gene"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_variant", b"_variant"] - ) -> typing_extensions.Literal["variant"] | None: ... + self, oneof_group: typing.Literal["_variant", b"_variant"] + ) -> typing.Literal["variant"] | None: ... global___VariantAnnotation = VariantAnnotation +@typing.final class GeneRelatedAnnotation(google.protobuf.message.Message): """ Gene-related annotation. @@ -851,7 +862,7 @@ class GeneRelatedAnnotation(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_consequences", b"_consequences", "_constraints", @@ -872,7 +883,7 @@ class GeneRelatedAnnotation(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_consequences", b"_consequences", "_constraints", @@ -893,23 +904,24 @@ class GeneRelatedAnnotation(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_consequences", b"_consequences"] - ) -> typing_extensions.Literal["consequences"] | None: ... + self, oneof_group: typing.Literal["_consequences", b"_consequences"] + ) -> typing.Literal["consequences"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_constraints", b"_constraints"] - ) -> typing_extensions.Literal["constraints"] | None: ... + self, oneof_group: typing.Literal["_constraints", b"_constraints"] + ) -> typing.Literal["constraints"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_identity", b"_identity"] - ) -> typing_extensions.Literal["identity"] | None: ... + self, oneof_group: typing.Literal["_identity", b"_identity"] + ) -> typing.Literal["identity"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_phenotypes", b"_phenotypes"] - ) -> typing_extensions.Literal["phenotypes"] | None: ... + self, oneof_group: typing.Literal["_phenotypes", b"_phenotypes"] + ) -> typing.Literal["phenotypes"] | None: ... global___GeneRelatedAnnotation = GeneRelatedAnnotation +@typing.final class GeneIdentity(google.protobuf.message.Message): """Gene identity related information.""" @@ -928,12 +940,12 @@ class GeneIdentity(google.protobuf.message.Message): gene_symbol: builtins.str = ..., ) -> None: ... def ClearField( - self, - field_name: typing_extensions.Literal["gene_symbol", b"gene_symbol", "hgnc_id", b"hgnc_id"], + self, field_name: typing.Literal["gene_symbol", b"gene_symbol", "hgnc_id", b"hgnc_id"] ) -> None: ... global___GeneIdentity = GeneIdentity +@typing.final class GeneRelatedConsequences(google.protobuf.message.Message): """/ Gene-related consequences of a variant.""" @@ -951,13 +963,6 @@ class GeneRelatedConsequences(google.protobuf.message.Message): """HGVS. {c,n} code of variant.""" hgvs_p: builtins.str """HGVS.p code of variant.""" - @property - def consequences( - self, - ) -> google.protobuf.internal.containers.RepeatedScalarFieldContainer[ - seqvars.protos.query_pb2.Consequence.ValueType - ]: - """Predicted variant consequences.""" tx_accession: builtins.str """Transcript accession without version.""" tx_version: builtins.int @@ -968,6 +973,14 @@ class GeneRelatedConsequences(google.protobuf.message.Message): """Exon/intron number (1-based).""" rank_total: builtins.int """Exon/intron total count.""" + @property + def consequences( + self, + ) -> google.protobuf.internal.containers.RepeatedScalarFieldContainer[ + seqvars.protos.query_pb2.Consequence.ValueType + ]: + """Predicted variant consequences.""" + def __init__( self, *, @@ -984,7 +997,7 @@ class GeneRelatedConsequences(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_hgvs_p", b"_hgvs_p", "_hgvs_t", @@ -1013,7 +1026,7 @@ class GeneRelatedConsequences(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_hgvs_p", b"_hgvs_p", "_hgvs_t", @@ -1046,31 +1059,32 @@ class GeneRelatedConsequences(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_hgvs_p", b"_hgvs_p"] - ) -> typing_extensions.Literal["hgvs_p"] | None: ... + self, oneof_group: typing.Literal["_hgvs_p", b"_hgvs_p"] + ) -> typing.Literal["hgvs_p"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_hgvs_t", b"_hgvs_t"] - ) -> typing_extensions.Literal["hgvs_t"] | None: ... + self, oneof_group: typing.Literal["_hgvs_t", b"_hgvs_t"] + ) -> typing.Literal["hgvs_t"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_rank_ord", b"_rank_ord"] - ) -> typing_extensions.Literal["rank_ord"] | None: ... + self, oneof_group: typing.Literal["_rank_ord", b"_rank_ord"] + ) -> typing.Literal["rank_ord"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_rank_total", b"_rank_total"] - ) -> typing_extensions.Literal["rank_total"] | None: ... + self, oneof_group: typing.Literal["_rank_total", b"_rank_total"] + ) -> typing.Literal["rank_total"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_tx_accession", b"_tx_accession"] - ) -> typing_extensions.Literal["tx_accession"] | None: ... + self, oneof_group: typing.Literal["_tx_accession", b"_tx_accession"] + ) -> typing.Literal["tx_accession"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_tx_version", b"_tx_version"] - ) -> typing_extensions.Literal["tx_version"] | None: ... + self, oneof_group: typing.Literal["_tx_version", b"_tx_version"] + ) -> typing.Literal["tx_version"] | None: ... global___GeneRelatedConsequences = GeneRelatedConsequences +@typing.final class GeneRelatedPhenotypes(google.protobuf.message.Message): """Phenotype-related information, if any.""" @@ -1102,7 +1116,7 @@ class GeneRelatedPhenotypes(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "is_acmg_sf", b"is_acmg_sf", "is_disease_gene", @@ -1114,6 +1128,7 @@ class GeneRelatedPhenotypes(google.protobuf.message.Message): global___GeneRelatedPhenotypes = GeneRelatedPhenotypes +@typing.final class GeneRelatedConstraints(google.protobuf.message.Message): """Gene-wise constraints.""" @@ -1155,7 +1170,7 @@ class GeneRelatedConstraints(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_clingen", b"_clingen", "_decipher", @@ -1180,7 +1195,7 @@ class GeneRelatedConstraints(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_clingen", b"_clingen", "_decipher", @@ -1205,27 +1220,28 @@ class GeneRelatedConstraints(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_clingen", b"_clingen"] - ) -> typing_extensions.Literal["clingen"] | None: ... + self, oneof_group: typing.Literal["_clingen", b"_clingen"] + ) -> typing.Literal["clingen"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_decipher", b"_decipher"] - ) -> typing_extensions.Literal["decipher"] | None: ... + self, oneof_group: typing.Literal["_decipher", b"_decipher"] + ) -> typing.Literal["decipher"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_gnomad", b"_gnomad"] - ) -> typing_extensions.Literal["gnomad"] | None: ... + self, oneof_group: typing.Literal["_gnomad", b"_gnomad"] + ) -> typing.Literal["gnomad"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_rcnv", b"_rcnv"] - ) -> typing_extensions.Literal["rcnv"] | None: ... + self, oneof_group: typing.Literal["_rcnv", b"_rcnv"] + ) -> typing.Literal["rcnv"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_shet", b"_shet"] - ) -> typing_extensions.Literal["shet"] | None: ... + self, oneof_group: typing.Literal["_shet", b"_shet"] + ) -> typing.Literal["shet"] | None: ... global___GeneRelatedConstraints = GeneRelatedConstraints +@typing.final class GnomadConstraints(google.protobuf.message.Message): """gnomAD constraint information.""" @@ -1273,7 +1289,7 @@ class GnomadConstraints(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "mis_z", b"mis_z", "oe_lof", @@ -1297,6 +1313,7 @@ class GnomadConstraints(google.protobuf.message.Message): global___GnomadConstraints = GnomadConstraints +@typing.final class DecipherConstraints(google.protobuf.message.Message): """DECIPHER constraint information.""" @@ -1315,11 +1332,12 @@ class DecipherConstraints(google.protobuf.message.Message): hi_index: builtins.float = ..., ) -> None: ... def ClearField( - self, field_name: typing_extensions.Literal["hi_index", b"hi_index", "p_hi", b"p_hi"] + self, field_name: typing.Literal["hi_index", b"hi_index", "p_hi", b"p_hi"] ) -> None: ... global___DecipherConstraints = DecipherConstraints +@typing.final class RcnvConstraints(google.protobuf.message.Message): """RCNV constraint information from PMID:35917817""" @@ -1338,11 +1356,12 @@ class RcnvConstraints(google.protobuf.message.Message): p_triplo: builtins.float = ..., ) -> None: ... def ClearField( - self, field_name: typing_extensions.Literal["p_haplo", b"p_haplo", "p_triplo", b"p_triplo"] + self, field_name: typing.Literal["p_haplo", b"p_haplo", "p_triplo", b"p_triplo"] ) -> None: ... global___RcnvConstraints = RcnvConstraints +@typing.final class ShetConstraints(google.protobuf.message.Message): """sHET constraint information from PMID:31004148""" @@ -1356,10 +1375,11 @@ class ShetConstraints(google.protobuf.message.Message): *, s_het: builtins.float = ..., ) -> None: ... - def ClearField(self, field_name: typing_extensions.Literal["s_het", b"s_het"]) -> None: ... + def ClearField(self, field_name: typing.Literal["s_het", b"s_het"]) -> None: ... global___ShetConstraints = ShetConstraints +@typing.final class ClingenDosageAnnotation(google.protobuf.message.Message): """ClinGen dosage annotation.""" @@ -1378,11 +1398,12 @@ class ClingenDosageAnnotation(google.protobuf.message.Message): triplo: global___ClingenDosageScore.ValueType = ..., ) -> None: ... def ClearField( - self, field_name: typing_extensions.Literal["haplo", b"haplo", "triplo", b"triplo"] + self, field_name: typing.Literal["haplo", b"haplo", "triplo", b"triplo"] ) -> None: ... global___ClingenDosageAnnotation = ClingenDosageAnnotation +@typing.final class VariantRelatedAnnotation(google.protobuf.message.Message): """ Variant-related annotation. @@ -1422,7 +1443,7 @@ class VariantRelatedAnnotation(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_clinvar", b"_clinvar", "_dbids", @@ -1443,7 +1464,7 @@ class VariantRelatedAnnotation(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_clinvar", b"_clinvar", "_dbids", @@ -1464,23 +1485,24 @@ class VariantRelatedAnnotation(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_clinvar", b"_clinvar"] - ) -> typing_extensions.Literal["clinvar"] | None: ... + self, oneof_group: typing.Literal["_clinvar", b"_clinvar"] + ) -> typing.Literal["clinvar"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_dbids", b"_dbids"] - ) -> typing_extensions.Literal["dbids"] | None: ... + self, oneof_group: typing.Literal["_dbids", b"_dbids"] + ) -> typing.Literal["dbids"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_frequency", b"_frequency"] - ) -> typing_extensions.Literal["frequency"] | None: ... + self, oneof_group: typing.Literal["_frequency", b"_frequency"] + ) -> typing.Literal["frequency"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_scores", b"_scores"] - ) -> typing_extensions.Literal["scores"] | None: ... + self, oneof_group: typing.Literal["_scores", b"_scores"] + ) -> typing.Literal["scores"] | None: ... global___VariantRelatedAnnotation = VariantRelatedAnnotation +@typing.final class FrequencyAnnotation(google.protobuf.message.Message): """Population frequency information.""" @@ -1522,7 +1544,7 @@ class FrequencyAnnotation(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_gnomad_exomes", b"_gnomad_exomes", "_gnomad_genomes", @@ -1547,7 +1569,7 @@ class FrequencyAnnotation(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_gnomad_exomes", b"_gnomad_exomes", "_gnomad_genomes", @@ -1572,27 +1594,28 @@ class FrequencyAnnotation(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_gnomad_exomes", b"_gnomad_exomes"] - ) -> typing_extensions.Literal["gnomad_exomes"] | None: ... + self, oneof_group: typing.Literal["_gnomad_exomes", b"_gnomad_exomes"] + ) -> typing.Literal["gnomad_exomes"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_gnomad_genomes", b"_gnomad_genomes"] - ) -> typing_extensions.Literal["gnomad_genomes"] | None: ... + self, oneof_group: typing.Literal["_gnomad_genomes", b"_gnomad_genomes"] + ) -> typing.Literal["gnomad_genomes"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_gnomad_mtdna", b"_gnomad_mtdna"] - ) -> typing_extensions.Literal["gnomad_mtdna"] | None: ... + self, oneof_group: typing.Literal["_gnomad_mtdna", b"_gnomad_mtdna"] + ) -> typing.Literal["gnomad_mtdna"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_helixmtdb", b"_helixmtdb"] - ) -> typing_extensions.Literal["helixmtdb"] | None: ... + self, oneof_group: typing.Literal["_helixmtdb", b"_helixmtdb"] + ) -> typing.Literal["helixmtdb"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_inhouse", b"_inhouse"] - ) -> typing_extensions.Literal["inhouse"] | None: ... + self, oneof_group: typing.Literal["_inhouse", b"_inhouse"] + ) -> typing.Literal["inhouse"] | None: ... global___FrequencyAnnotation = FrequencyAnnotation +@typing.final class NuclearFrequency(google.protobuf.message.Message): """gnomAD and in-house frequency information.""" @@ -1624,13 +1647,14 @@ class NuclearFrequency(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "af", b"af", "an", b"an", "hemialt", b"hemialt", "het", b"het", "homalt", b"homalt" ], ) -> None: ... global___NuclearFrequency = NuclearFrequency +@typing.final class MitochondrialFrequency(google.protobuf.message.Message): """Mitochondrial frequency information.""" @@ -1658,13 +1682,12 @@ class MitochondrialFrequency(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ - "af", b"af", "an", b"an", "het", b"het", "homalt", b"homalt" - ], + field_name: typing.Literal["af", b"af", "an", b"an", "het", b"het", "homalt", b"homalt"], ) -> None: ... global___MitochondrialFrequency = MitochondrialFrequency +@typing.final class DbIds(google.protobuf.message.Message): """Database identifiers.""" @@ -1679,19 +1702,18 @@ class DbIds(google.protobuf.message.Message): dbsnp_id: builtins.str | None = ..., ) -> None: ... def HasField( - self, - field_name: typing_extensions.Literal["_dbsnp_id", b"_dbsnp_id", "dbsnp_id", b"dbsnp_id"], + self, field_name: typing.Literal["_dbsnp_id", b"_dbsnp_id", "dbsnp_id", b"dbsnp_id"] ) -> builtins.bool: ... def ClearField( - self, - field_name: typing_extensions.Literal["_dbsnp_id", b"_dbsnp_id", "dbsnp_id", b"dbsnp_id"], + self, field_name: typing.Literal["_dbsnp_id", b"_dbsnp_id", "dbsnp_id", b"dbsnp_id"] ) -> None: ... def WhichOneof( - self, oneof_group: typing_extensions.Literal["_dbsnp_id", b"_dbsnp_id"] - ) -> typing_extensions.Literal["dbsnp_id"] | None: ... + self, oneof_group: typing.Literal["_dbsnp_id", b"_dbsnp_id"] + ) -> typing.Literal["dbsnp_id"] | None: ... global___DbIds = DbIds +@typing.final class ClinvarAnnotation(google.protobuf.message.Message): """ClinVar-related annotation.""" @@ -1719,7 +1741,7 @@ class ClinvarAnnotation(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "effective_germline_significance_description", b"effective_germline_significance_description", "germline_review_status", @@ -1733,6 +1755,7 @@ class ClinvarAnnotation(google.protobuf.message.Message): global___ClinvarAnnotation = ClinvarAnnotation +@typing.final class ScoreAnnotations(google.protobuf.message.Message): """Score annotations.""" @@ -1750,10 +1773,11 @@ class ScoreAnnotations(google.protobuf.message.Message): *, entries: collections.abc.Iterable[global___ScoreEntry] | None = ..., ) -> None: ... - def ClearField(self, field_name: typing_extensions.Literal["entries", b"entries"]) -> None: ... + def ClearField(self, field_name: typing.Literal["entries", b"entries"]) -> None: ... global___ScoreAnnotations = ScoreAnnotations +@typing.final class ScoreEntry(google.protobuf.message.Message): """Score entry.""" @@ -1774,20 +1798,18 @@ class ScoreEntry(google.protobuf.message.Message): value: google.protobuf.struct_pb2.Value | None = ..., ) -> None: ... def HasField( - self, field_name: typing_extensions.Literal["_value", b"_value", "value", b"value"] + self, field_name: typing.Literal["_value", b"_value", "value", b"value"] ) -> builtins.bool: ... def ClearField( - self, - field_name: typing_extensions.Literal[ - "_value", b"_value", "key", b"key", "value", b"value" - ], + self, field_name: typing.Literal["_value", b"_value", "key", b"key", "value", b"value"] ) -> None: ... def WhichOneof( - self, oneof_group: typing_extensions.Literal["_value", b"_value"] - ) -> typing_extensions.Literal["value"] | None: ... + self, oneof_group: typing.Literal["_value", b"_value"] + ) -> typing.Literal["value"] | None: ... global___ScoreEntry = ScoreEntry +@typing.final class CallRelatedAnnotation(google.protobuf.message.Message): """ Gene-related annotation. @@ -1811,12 +1833,11 @@ class CallRelatedAnnotation(google.protobuf.message.Message): *, call_infos: collections.abc.Iterable[global___SampleCallInfo] | None = ..., ) -> None: ... - def ClearField( - self, field_name: typing_extensions.Literal["call_infos", b"call_infos"] - ) -> None: ... + def ClearField(self, field_name: typing.Literal["call_infos", b"call_infos"]) -> None: ... global___CallRelatedAnnotation = CallRelatedAnnotation +@typing.final class SampleCallInfo(google.protobuf.message.Message): """Store call information for one sample.""" @@ -1852,7 +1873,7 @@ class SampleCallInfo(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_ad", b"_ad", "_dp", @@ -1877,7 +1898,7 @@ class SampleCallInfo(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_ad", b"_ad", "_dp", @@ -1904,23 +1925,23 @@ class SampleCallInfo(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_ad", b"_ad"] - ) -> typing_extensions.Literal["ad"] | None: ... + self, oneof_group: typing.Literal["_ad", b"_ad"] + ) -> typing.Literal["ad"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_dp", b"_dp"] - ) -> typing_extensions.Literal["dp"] | None: ... + self, oneof_group: typing.Literal["_dp", b"_dp"] + ) -> typing.Literal["dp"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_genotype", b"_genotype"] - ) -> typing_extensions.Literal["genotype"] | None: ... + self, oneof_group: typing.Literal["_genotype", b"_genotype"] + ) -> typing.Literal["genotype"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_gq", b"_gq"] - ) -> typing_extensions.Literal["gq"] | None: ... + self, oneof_group: typing.Literal["_gq", b"_gq"] + ) -> typing.Literal["gq"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_ps", b"_ps"] - ) -> typing_extensions.Literal["ps"] | None: ... + self, oneof_group: typing.Literal["_ps", b"_ps"] + ) -> typing.Literal["ps"] | None: ... global___SampleCallInfo = SampleCallInfo diff --git a/backend/seqvars/protos/query_pb2.py b/backend/seqvars/protos/query_pb2.py index ebc1db074..da659c91b 100644 --- a/backend/seqvars/protos/query_pb2.py +++ b/backend/seqvars/protos/query_pb2.py @@ -1,64 +1,70 @@ # -*- coding: utf-8 -*- # Generated by the protocol buffer compiler. DO NOT EDIT! +# NO CHECKED-IN PROTOBUF GENCODE # source: seqvars/protos/query.proto +# Protobuf Python Version: 5.28.1 """Generated protocol buffer code.""" from google.protobuf import descriptor as _descriptor from google.protobuf import descriptor_pool as _descriptor_pool +from google.protobuf import runtime_version as _runtime_version from google.protobuf import symbol_database as _symbol_database from google.protobuf.internal import builder as _builder +_runtime_version.ValidateProtobufRuntimeVersion( + _runtime_version.Domain.PUBLIC, 5, 28, 1, "", "seqvars/protos/query.proto" +) # @@protoc_insertion_point(imports) _sym_db = _symbol_database.Default() DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile( - b'\n\x1aseqvars/protos/query.proto\x12\x11seqvars.pbs.query"\x85\x01\n\x14SampleGenotypeChoice\x12\x0e\n\x06sample\x18\x01 \x01(\t\x12\x33\n\x08genotype\x18\x02 \x01(\x0e\x32!.seqvars.pbs.query.GenotypeChoice\x12\x17\n\x0finclude_no_call\x18\x03 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-_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, globals()) -_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, "seqvars.protos.query_pb2", globals()) -if _descriptor._USE_C_DESCRIPTORS == False: - - DESCRIPTOR._options = None - _RECESSIVEMODE._serialized_start = 2625 - _RECESSIVEMODE._serialized_end = 2798 - _GENOTYPECHOICE._serialized_start = 2801 - _GENOTYPECHOICE._serialized_end = 3150 - _VARIANTTYPE._serialized_start = 3153 - _VARIANTTYPE._serialized_end = 3303 - _TRANSCRIPTTYPE._serialized_start = 3305 - _TRANSCRIPTTYPE._serialized_end = 3414 - _CONSEQUENCE._serialized_start = 3417 - _CONSEQUENCE._serialized_end = 5415 - _CLINVARGERMLINEAGGREGATEDESCRIPTION._serialized_start = 5418 - _CLINVARGERMLINEAGGREGATEDESCRIPTION._serialized_end = 5804 - _SAMPLEGENOTYPECHOICE._serialized_start = 50 - _SAMPLEGENOTYPECHOICE._serialized_end = 183 - _QUERYSETTINGSGENOTYPE._serialized_start = 186 - _QUERYSETTINGSGENOTYPE._serialized_end = 334 - _SAMPLEQUALITYSETTINGS._serialized_start = 337 - _SAMPLEQUALITYSETTINGS._serialized_end = 607 - _QUERYSETTINGSQUALITY._serialized_start = 609 - _QUERYSETTINGSQUALITY._serialized_end = 699 - _NUCLEARFREQUENCYSETTINGS._serialized_start = 702 - _NUCLEARFREQUENCYSETTINGS._serialized_end = 881 - _MITOCHONDRIALFREQUENCYSETTINGS._serialized_start = 884 - _MITOCHONDRIALFREQUENCYSETTINGS._serialized_end = 1033 - _INHOUSEFREQUENCYSETTINGS._serialized_start = 1036 - _INHOUSEFREQUENCYSETTINGS._serialized_end = 1227 - _QUERYSETTINGSFREQUENCY._serialized_start = 1230 - _QUERYSETTINGSFREQUENCY._serialized_end = 1596 - _QUERYSETTINGSCONSEQUENCE._serialized_start = 1599 - _QUERYSETTINGSCONSEQUENCE._serialized_end = 1847 - _RANGE._serialized_start = 1849 - _RANGE._serialized_end = 1885 - _GENOMICREGION._serialized_start = 1887 - _GENOMICREGION._serialized_end = 1973 - _QUERYSETTINGSLOCUS._serialized_start = 1975 - _QUERYSETTINGSLOCUS._serialized_end = 2068 - _QUERYSETTINGSCLINVAR._serialized_start = 2071 - _QUERYSETTINGSCLINVAR._serialized_end = 2250 - _CASEQUERY._serialized_start = 2253 - _CASEQUERY._serialized_end = 2622 +_globals = globals() +_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) +_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, "seqvars.protos.query_pb2", _globals) +if not _descriptor._USE_C_DESCRIPTORS: + DESCRIPTOR._loaded_options = None + _globals["_RECESSIVEMODE"]._serialized_start = 2625 + _globals["_RECESSIVEMODE"]._serialized_end = 2798 + _globals["_GENOTYPECHOICE"]._serialized_start = 2801 + _globals["_GENOTYPECHOICE"]._serialized_end = 3150 + _globals["_VARIANTTYPE"]._serialized_start = 3153 + _globals["_VARIANTTYPE"]._serialized_end = 3303 + _globals["_TRANSCRIPTTYPE"]._serialized_start = 3305 + _globals["_TRANSCRIPTTYPE"]._serialized_end = 3414 + _globals["_CONSEQUENCE"]._serialized_start = 3417 + _globals["_CONSEQUENCE"]._serialized_end = 5737 + _globals["_CLINVARGERMLINEAGGREGATEDESCRIPTION"]._serialized_start = 5740 + _globals["_CLINVARGERMLINEAGGREGATEDESCRIPTION"]._serialized_end = 6126 + _globals["_SAMPLEGENOTYPECHOICE"]._serialized_start = 50 + _globals["_SAMPLEGENOTYPECHOICE"]._serialized_end = 183 + _globals["_QUERYSETTINGSGENOTYPE"]._serialized_start = 186 + _globals["_QUERYSETTINGSGENOTYPE"]._serialized_end = 334 + _globals["_SAMPLEQUALITYSETTINGS"]._serialized_start = 337 + _globals["_SAMPLEQUALITYSETTINGS"]._serialized_end = 607 + _globals["_QUERYSETTINGSQUALITY"]._serialized_start = 609 + _globals["_QUERYSETTINGSQUALITY"]._serialized_end = 699 + _globals["_NUCLEARFREQUENCYSETTINGS"]._serialized_start = 702 + _globals["_NUCLEARFREQUENCYSETTINGS"]._serialized_end = 881 + _globals["_MITOCHONDRIALFREQUENCYSETTINGS"]._serialized_start = 884 + _globals["_MITOCHONDRIALFREQUENCYSETTINGS"]._serialized_end = 1033 + _globals["_INHOUSEFREQUENCYSETTINGS"]._serialized_start = 1036 + _globals["_INHOUSEFREQUENCYSETTINGS"]._serialized_end = 1227 + _globals["_QUERYSETTINGSFREQUENCY"]._serialized_start = 1230 + _globals["_QUERYSETTINGSFREQUENCY"]._serialized_end = 1596 + _globals["_QUERYSETTINGSCONSEQUENCE"]._serialized_start = 1599 + _globals["_QUERYSETTINGSCONSEQUENCE"]._serialized_end = 1847 + _globals["_RANGE"]._serialized_start = 1849 + _globals["_RANGE"]._serialized_end = 1885 + _globals["_GENOMICREGION"]._serialized_start = 1887 + _globals["_GENOMICREGION"]._serialized_end = 1973 + _globals["_QUERYSETTINGSLOCUS"]._serialized_start = 1975 + _globals["_QUERYSETTINGSLOCUS"]._serialized_end = 2068 + _globals["_QUERYSETTINGSCLINVAR"]._serialized_start = 2071 + _globals["_QUERYSETTINGSCLINVAR"]._serialized_end = 2250 + _globals["_CASEQUERY"]._serialized_start = 2253 + _globals["_CASEQUERY"]._serialized_end = 2622 # @@protoc_insertion_point(module_scope) diff --git a/backend/seqvars/protos/query_pb2.pyi b/backend/seqvars/protos/query_pb2.pyi index 4adb55867..b6c946d37 100644 --- a/backend/seqvars/protos/query_pb2.pyi +++ b/backend/seqvars/protos/query_pb2.pyi @@ -26,7 +26,7 @@ class _RecessiveMode: class _RecessiveModeEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_RecessiveMode.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor RECESSIVE_MODE_UNSPECIFIED: _RecessiveMode.ValueType # 0 """Unknown recessive mode.""" @@ -61,7 +61,7 @@ class _GenotypeChoice: class _GenotypeChoiceEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_GenotypeChoice.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor GENOTYPE_CHOICE_UNSPECIFIED: _GenotypeChoice.ValueType # 0 """Unknown genotype.""" @@ -120,7 +120,7 @@ class _VariantType: class _VariantTypeEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_VariantType.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor VARIANT_TYPE_UNSPECIFIED: _VariantType.ValueType # 0 """Unknown variant type""" @@ -155,7 +155,7 @@ class _TranscriptType: class _TranscriptTypeEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_TranscriptType.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor TRANSCRIPT_TYPE_UNSPECIFIED: _TranscriptType.ValueType # 0 """Unknown transcript type.""" @@ -182,7 +182,7 @@ class _Consequence: class _ConsequenceEnumTypeWrapper( google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_Consequence.ValueType], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor CONSEQUENCE_UNSPECIFIED: _Consequence.ValueType # 0 """Unknown consequence. @@ -231,7 +231,15 @@ class _ConsequenceEnumTypeWrapper( CONSEQUENCE_RARE_AMINO_ACID_VARIANT: _Consequence.ValueType # 45 """Rare amino acid variant""" CONSEQUENCE_PROTEIN_ALTERING_VARIANT: _Consequence.ValueType # 46 - """Protein altering variant + """Protein altering variant""" + CONSEQUENCE_INFRAME_DELETION: _Consequence.ValueType # 49 + """Inframe deletion""" + CONSEQUENCE_INFRAME_INSERTION: _Consequence.ValueType # 50 + """Inframe insertion""" + CONSEQUENCE_SELENOCYSTEINE_GAIN: _Consequence.ValueType # 51 + """Selenocysteine gain""" + CONSEQUENCE_SELENOCYSTEINE_LOSS: _Consequence.ValueType # 52 + """Selenocysteine loss low impact """ @@ -250,7 +258,9 @@ class _ConsequenceEnumTypeWrapper( CONSEQUENCE_STOP_RETAINED_VARIANT: _Consequence.ValueType # 22 """Stop retained variant.""" CONSEQUENCE_SYNONYMOUS_VARIANT: _Consequence.ValueType # 23 - """Synonymous variant. + """Synonymous variant.""" + CONSEQUENCE_INCOMPLETE_TERMINAL_CODON_VARIANT: _Consequence.ValueType # 53 + """Incomplete terminal codon variant modifier """ @@ -262,14 +272,20 @@ class _ConsequenceEnumTypeWrapper( """5' UTR exon variant.""" CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT: _Consequence.ValueType # 27 """5' UTR intron variant.""" + CONSEQUENCE_FIVE_PRIME_UTR_VARIANT: _Consequence.ValueType # 54 + """5' UTR variant.""" CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT: _Consequence.ValueType # 28 """3' UTR exon variant.""" CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT: _Consequence.ValueType # 29 """3' UTR intron variant.""" + CONSEQUENCE_THREE_PRIME_UTR_VARIANT: _Consequence.ValueType # 55 + """3' UTR variant.""" CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT: _Consequence.ValueType # 30 """Non-coding transcript exon variant.""" CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT: _Consequence.ValueType # 31 """Non-coding transcript intron variant.""" + CONSEQUENCE_NON_CODING_TRANSCRIPT_VARIANT: _Consequence.ValueType # 56 + """Non-coding transcript variant.""" CONSEQUENCE_CODING_TRANSCRIPT_INTRON_VARIANT: _Consequence.ValueType # 48 """Coding transcript intron variant.""" CONSEQUENCE_UPSTREAM_GENE_VARIANT: _Consequence.ValueType # 32 @@ -345,7 +361,15 @@ CONSEQUENCE_MISSENSE_VARIANT: Consequence.ValueType # 16 CONSEQUENCE_RARE_AMINO_ACID_VARIANT: Consequence.ValueType # 45 """Rare amino acid variant""" CONSEQUENCE_PROTEIN_ALTERING_VARIANT: Consequence.ValueType # 46 -"""Protein altering variant +"""Protein altering variant""" +CONSEQUENCE_INFRAME_DELETION: Consequence.ValueType # 49 +"""Inframe deletion""" +CONSEQUENCE_INFRAME_INSERTION: Consequence.ValueType # 50 +"""Inframe insertion""" +CONSEQUENCE_SELENOCYSTEINE_GAIN: Consequence.ValueType # 51 +"""Selenocysteine gain""" +CONSEQUENCE_SELENOCYSTEINE_LOSS: Consequence.ValueType # 52 +"""Selenocysteine loss low impact """ @@ -364,7 +388,9 @@ CONSEQUENCE_START_RETAINED_VARIANT: Consequence.ValueType # 21 CONSEQUENCE_STOP_RETAINED_VARIANT: Consequence.ValueType # 22 """Stop retained variant.""" CONSEQUENCE_SYNONYMOUS_VARIANT: Consequence.ValueType # 23 -"""Synonymous variant. +"""Synonymous variant.""" +CONSEQUENCE_INCOMPLETE_TERMINAL_CODON_VARIANT: Consequence.ValueType # 53 +"""Incomplete terminal codon variant modifier """ @@ -376,14 +402,20 @@ CONSEQUENCE_FIVE_PRIME_UTR_EXON_VARIANT: Consequence.ValueType # 26 """5' UTR exon variant.""" CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT: Consequence.ValueType # 27 """5' UTR intron variant.""" +CONSEQUENCE_FIVE_PRIME_UTR_VARIANT: Consequence.ValueType # 54 +"""5' UTR variant.""" CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT: Consequence.ValueType # 28 """3' UTR exon variant.""" CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT: Consequence.ValueType # 29 """3' UTR intron variant.""" +CONSEQUENCE_THREE_PRIME_UTR_VARIANT: Consequence.ValueType # 55 +"""3' UTR variant.""" CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT: Consequence.ValueType # 30 """Non-coding transcript exon variant.""" CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT: Consequence.ValueType # 31 """Non-coding transcript intron variant.""" +CONSEQUENCE_NON_CODING_TRANSCRIPT_VARIANT: Consequence.ValueType # 56 +"""Non-coding transcript variant.""" CONSEQUENCE_CODING_TRANSCRIPT_INTRON_VARIANT: Consequence.ValueType # 48 """Coding transcript intron variant.""" CONSEQUENCE_UPSTREAM_GENE_VARIANT: Consequence.ValueType # 32 @@ -419,7 +451,7 @@ class _ClinvarGermlineAggregateDescriptionEnumTypeWrapper( _ClinvarGermlineAggregateDescription.ValueType ], builtins.type, -): # noqa: F821 +): DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_UNSPECIFIED: ( _ClinvarGermlineAggregateDescription.ValueType @@ -476,6 +508,7 @@ CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_BENIGN: ClinvarGermlineAggregateDescripti """Benign.""" global___ClinvarGermlineAggregateDescription = ClinvarGermlineAggregateDescription +@typing.final class SampleGenotypeChoice(google.protobuf.message.Message): """Genotype choice for one sample.""" @@ -503,7 +536,7 @@ class SampleGenotypeChoice(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "enabled", b"enabled", "genotype", @@ -517,6 +550,7 @@ class SampleGenotypeChoice(google.protobuf.message.Message): global___SampleGenotypeChoice = SampleGenotypeChoice +@typing.final class QuerySettingsGenotype(google.protobuf.message.Message): """Genotype-related filter settings.""" @@ -542,13 +576,14 @@ class QuerySettingsGenotype(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "recessive_mode", b"recessive_mode", "sample_genotypes", b"sample_genotypes" ], ) -> None: ... global___QuerySettingsGenotype = QuerySettingsGenotype +@typing.final class SampleQualitySettings(google.protobuf.message.Message): """Quality settings for one sample.""" @@ -592,7 +627,7 @@ class SampleQualitySettings(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_ad", b"_max_ad", "_min_ab", @@ -621,7 +656,7 @@ class SampleQualitySettings(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_ad", b"_max_ad", "_min_ab", @@ -654,31 +689,32 @@ class SampleQualitySettings(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_ad", b"_max_ad"] - ) -> typing_extensions.Literal["max_ad"] | None: ... + self, oneof_group: typing.Literal["_max_ad", b"_max_ad"] + ) -> typing.Literal["max_ad"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_min_ab", b"_min_ab"] - ) -> typing_extensions.Literal["min_ab"] | None: ... + self, oneof_group: typing.Literal["_min_ab", b"_min_ab"] + ) -> typing.Literal["min_ab"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_min_ad", b"_min_ad"] - ) -> typing_extensions.Literal["min_ad"] | None: ... + self, oneof_group: typing.Literal["_min_ad", b"_min_ad"] + ) -> typing.Literal["min_ad"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_min_dp_het", b"_min_dp_het"] - ) -> typing_extensions.Literal["min_dp_het"] | None: ... + self, oneof_group: typing.Literal["_min_dp_het", b"_min_dp_het"] + ) -> typing.Literal["min_dp_het"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_min_dp_hom", b"_min_dp_hom"] - ) -> typing_extensions.Literal["min_dp_hom"] | None: ... + self, oneof_group: typing.Literal["_min_dp_hom", b"_min_dp_hom"] + ) -> typing.Literal["min_dp_hom"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_min_gq", b"_min_gq"] - ) -> typing_extensions.Literal["min_gq"] | None: ... + self, oneof_group: typing.Literal["_min_gq", b"_min_gq"] + ) -> typing.Literal["min_gq"] | None: ... global___SampleQualitySettings = SampleQualitySettings +@typing.final class QuerySettingsQuality(google.protobuf.message.Message): """Per-sample quality filter settings.""" @@ -699,11 +735,12 @@ class QuerySettingsQuality(google.protobuf.message.Message): sample_qualities: collections.abc.Iterable[global___SampleQualitySettings] | None = ..., ) -> None: ... def ClearField( - self, field_name: typing_extensions.Literal["sample_qualities", b"sample_qualities"] + self, field_name: typing.Literal["sample_qualities", b"sample_qualities"] ) -> None: ... global___QuerySettingsQuality = QuerySettingsQuality +@typing.final class NuclearFrequencySettings(google.protobuf.message.Message): """gnomAD filter options.""" @@ -735,7 +772,7 @@ class NuclearFrequencySettings(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_af", b"_max_af", "_max_hemi", @@ -756,7 +793,7 @@ class NuclearFrequencySettings(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_af", b"_max_af", "_max_hemi", @@ -779,23 +816,24 @@ class NuclearFrequencySettings(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_af", b"_max_af"] - ) -> typing_extensions.Literal["max_af"] | None: ... + self, oneof_group: typing.Literal["_max_af", b"_max_af"] + ) -> typing.Literal["max_af"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_hemi", b"_max_hemi"] - ) -> typing_extensions.Literal["max_hemi"] | None: ... + self, oneof_group: typing.Literal["_max_hemi", b"_max_hemi"] + ) -> typing.Literal["max_hemi"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_het", b"_max_het"] - ) -> typing_extensions.Literal["max_het"] | None: ... + self, oneof_group: typing.Literal["_max_het", b"_max_het"] + ) -> typing.Literal["max_het"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_hom", b"_max_hom"] - ) -> typing_extensions.Literal["max_hom"] | None: ... + self, oneof_group: typing.Literal["_max_hom", b"_max_hom"] + ) -> typing.Literal["max_hom"] | None: ... global___NuclearFrequencySettings = NuclearFrequencySettings +@typing.final class MitochondrialFrequencySettings(google.protobuf.message.Message): """Mitochondrial filter options.""" @@ -823,7 +861,7 @@ class MitochondrialFrequencySettings(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_af", b"_max_af", "_max_het", @@ -840,7 +878,7 @@ class MitochondrialFrequencySettings(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_af", b"_max_af", "_max_het", @@ -859,19 +897,20 @@ class MitochondrialFrequencySettings(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_af", b"_max_af"] - ) -> typing_extensions.Literal["max_af"] | None: ... + self, oneof_group: typing.Literal["_max_af", b"_max_af"] + ) -> typing.Literal["max_af"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_het", b"_max_het"] - ) -> typing_extensions.Literal["max_het"] | None: ... + self, oneof_group: typing.Literal["_max_het", b"_max_het"] + ) -> typing.Literal["max_het"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_hom", b"_max_hom"] - ) -> typing_extensions.Literal["max_hom"] | None: ... + self, oneof_group: typing.Literal["_max_hom", b"_max_hom"] + ) -> typing.Literal["max_hom"] | None: ... global___MitochondrialFrequencySettings = MitochondrialFrequencySettings +@typing.final class InhouseFrequencySettings(google.protobuf.message.Message): """In-house filter options.""" @@ -903,7 +942,7 @@ class InhouseFrequencySettings(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_carriers", b"_max_carriers", "_max_hemi", @@ -924,7 +963,7 @@ class InhouseFrequencySettings(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_carriers", b"_max_carriers", "_max_hemi", @@ -947,23 +986,24 @@ class InhouseFrequencySettings(google.protobuf.message.Message): ) -> None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_carriers", b"_max_carriers"] - ) -> typing_extensions.Literal["max_carriers"] | None: ... + self, oneof_group: typing.Literal["_max_carriers", b"_max_carriers"] + ) -> typing.Literal["max_carriers"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_hemi", b"_max_hemi"] - ) -> typing_extensions.Literal["max_hemi"] | None: ... + self, oneof_group: typing.Literal["_max_hemi", b"_max_hemi"] + ) -> typing.Literal["max_hemi"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_het", b"_max_het"] - ) -> typing_extensions.Literal["max_het"] | None: ... + self, oneof_group: typing.Literal["_max_het", b"_max_het"] + ) -> typing.Literal["max_het"] | None: ... @typing.overload def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_hom", b"_max_hom"] - ) -> typing_extensions.Literal["max_hom"] | None: ... + self, oneof_group: typing.Literal["_max_hom", b"_max_hom"] + ) -> typing.Literal["max_hom"] | None: ... global___InhouseFrequencySettings = InhouseFrequencySettings +@typing.final class QuerySettingsFrequency(google.protobuf.message.Message): """Population frequency filter options.""" @@ -1005,7 +1045,7 @@ class QuerySettingsFrequency(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "gnomad_exomes", b"gnomad_exomes", "gnomad_genomes", @@ -1020,7 +1060,7 @@ class QuerySettingsFrequency(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "gnomad_exomes", b"gnomad_exomes", "gnomad_genomes", @@ -1036,6 +1076,7 @@ class QuerySettingsFrequency(google.protobuf.message.Message): global___QuerySettingsFrequency = QuerySettingsFrequency +@typing.final class QuerySettingsConsequence(google.protobuf.message.Message): """Consequence-related filter settings.""" @@ -1045,6 +1086,8 @@ class QuerySettingsConsequence(google.protobuf.message.Message): TRANSCRIPT_TYPES_FIELD_NUMBER: builtins.int CONSEQUENCES_FIELD_NUMBER: builtins.int MAX_DIST_TO_EXON_FIELD_NUMBER: builtins.int + max_dist_to_exon: builtins.int + """Maximal distance to next exon, if any""" @property def variant_types( self, @@ -1068,8 +1111,7 @@ class QuerySettingsConsequence(google.protobuf.message.Message): global___Consequence.ValueType ]: """List of consequences to consider""" - max_dist_to_exon: builtins.int - """Maximal distance to next exon, if any""" + def __init__( self, *, @@ -1080,13 +1122,13 @@ class QuerySettingsConsequence(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_dist_to_exon", b"_max_dist_to_exon", "max_dist_to_exon", b"max_dist_to_exon" ], ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "_max_dist_to_exon", b"_max_dist_to_exon", "consequences", @@ -1100,11 +1142,12 @@ class QuerySettingsConsequence(google.protobuf.message.Message): ], ) -> None: ... def WhichOneof( - self, oneof_group: typing_extensions.Literal["_max_dist_to_exon", b"_max_dist_to_exon"] - ) -> typing_extensions.Literal["max_dist_to_exon"] | None: ... + self, oneof_group: typing.Literal["_max_dist_to_exon", b"_max_dist_to_exon"] + ) -> typing.Literal["max_dist_to_exon"] | None: ... global___QuerySettingsConsequence = QuerySettingsConsequence +@typing.final class Range(google.protobuf.message.Message): """An 1-based integer range.""" @@ -1123,11 +1166,12 @@ class Range(google.protobuf.message.Message): stop: builtins.int = ..., ) -> None: ... def ClearField( - self, field_name: typing_extensions.Literal["start", b"start", "stop", b"stop"] + self, field_name: typing.Literal["start", b"start", "stop", b"stop"] ) -> None: ... global___Range = Range +@typing.final class GenomicRegion(google.protobuf.message.Message): """Genomic region.""" @@ -1148,20 +1192,18 @@ class GenomicRegion(google.protobuf.message.Message): range: global___Range | None = ..., ) -> None: ... def HasField( - self, field_name: typing_extensions.Literal["_range", b"_range", "range", b"range"] + self, field_name: typing.Literal["_range", b"_range", "range", b"range"] ) -> builtins.bool: ... def ClearField( - self, - field_name: typing_extensions.Literal[ - "_range", b"_range", "chrom", b"chrom", "range", b"range" - ], + self, field_name: typing.Literal["_range", b"_range", "chrom", b"chrom", "range", b"range"] ) -> None: ... def WhichOneof( - self, oneof_group: typing_extensions.Literal["_range", b"_range"] - ) -> typing_extensions.Literal["range"] | None: ... + self, oneof_group: typing.Literal["_range", b"_range"] + ) -> typing.Literal["range"] | None: ... global___GenomicRegion = GenomicRegion +@typing.final class QuerySettingsLocus(google.protobuf.message.Message): """Locus-related filter settings.""" @@ -1193,14 +1235,12 @@ class QuerySettingsLocus(google.protobuf.message.Message): genome_regions: collections.abc.Iterable[global___GenomicRegion] | None = ..., ) -> None: ... def ClearField( - self, - field_name: typing_extensions.Literal[ - "genes", b"genes", "genome_regions", b"genome_regions" - ], + self, field_name: typing.Literal["genes", b"genes", "genome_regions", b"genome_regions"] ) -> None: ... global___QuerySettingsLocus = QuerySettingsLocus +@typing.final class QuerySettingsClinVar(google.protobuf.message.Message): """Clinvar-related query settings.""" @@ -1211,6 +1251,8 @@ class QuerySettingsClinVar(google.protobuf.message.Message): ALLOW_CONFLICTING_INTERPRETATIONS_FIELD_NUMBER: builtins.int presence_required: builtins.bool """Wether to require ClinVar membership""" + allow_conflicting_interpretations: builtins.bool + """Whether to include conflicting interpretation ClinVar variants""" @property def germline_descriptions( self, @@ -1218,8 +1260,7 @@ class QuerySettingsClinVar(google.protobuf.message.Message): global___ClinvarGermlineAggregateDescription.ValueType ]: """The ClinVar germline aggregate description to include.""" - allow_conflicting_interpretations: builtins.bool - """Whether to include conflicting interpretation ClinVar variants""" + def __init__( self, *, @@ -1231,7 +1272,7 @@ class QuerySettingsClinVar(google.protobuf.message.Message): ) -> None: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "allow_conflicting_interpretations", b"allow_conflicting_interpretations", "germline_descriptions", @@ -1243,6 +1284,7 @@ class QuerySettingsClinVar(google.protobuf.message.Message): global___QuerySettingsClinVar = QuerySettingsClinVar +@typing.final class CaseQuery(google.protobuf.message.Message): """Store query information for one case.""" @@ -1290,7 +1332,7 @@ class CaseQuery(google.protobuf.message.Message): ) -> None: ... def HasField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "clinvar", b"clinvar", "consequence", @@ -1307,7 +1349,7 @@ class CaseQuery(google.protobuf.message.Message): ) -> builtins.bool: ... def ClearField( self, - field_name: typing_extensions.Literal[ + field_name: typing.Literal[ "clinvar", b"clinvar", "consequence", diff --git a/backend/seqvars/tests/snapshots/snap_test_factory_defaults.py b/backend/seqvars/tests/snapshots/snap_test_factory_defaults.py index be6d999a6..9656194fc 100644 --- a/backend/seqvars/tests/snapshots/snap_test_factory_defaults.py +++ b/backend/seqvars/tests/snapshots/snap_test_factory_defaults.py @@ -1999,6 +1999,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -2007,13 +2011,17 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "coding_transcript_intron_variant", "upstream_gene_variant", "downstream_gene_variant", @@ -2081,11 +2089,16 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", "splice_donor_region_variant", "splice_polypyrimidine_tract_variant", + "incomplete_terminal_codon_variant", ], "variant_types": ["snv", "indel", "mnv", "complex_substitution"], }, @@ -2120,6 +2133,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -2128,6 +2145,7 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "intron_variant", @@ -2165,6 +2183,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -2173,13 +2195,17 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "coding_transcript_intron_variant", "upstream_gene_variant", "downstream_gene_variant", @@ -4697,6 +4723,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -4705,13 +4735,17 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "coding_transcript_intron_variant", "upstream_gene_variant", "downstream_gene_variant", @@ -4779,11 +4813,16 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", "splice_donor_region_variant", "splice_polypyrimidine_tract_variant", + "incomplete_terminal_codon_variant", ], "variant_types": ["snv", "indel", "mnv", "complex_substitution"], }, @@ -4818,6 +4857,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -4826,6 +4869,7 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "intron_variant", @@ -4863,6 +4907,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -4871,13 +4919,17 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "coding_transcript_intron_variant", "upstream_gene_variant", "downstream_gene_variant", @@ -7395,6 +7447,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -7403,13 +7459,17 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "coding_transcript_intron_variant", "upstream_gene_variant", "downstream_gene_variant", @@ -7477,11 +7537,16 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", "splice_donor_region_variant", "splice_polypyrimidine_tract_variant", + "incomplete_terminal_codon_variant", ], "variant_types": ["snv", "indel", "mnv", "complex_substitution"], }, @@ -7516,6 +7581,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -7524,6 +7593,7 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "intron_variant", @@ -7561,6 +7631,10 @@ "missense_variant", "rare_amino_acid_variant", "protein_altering_variant", + "inframe_deletion", + "inframe_insertion", + "selenocysteine_gain", + "selenocysteine_loss", "splice_donor_5th_base_variant", "splice_region_variant", "exonic_splice_region_variant", @@ -7569,13 +7643,17 @@ "start_retained_variant", "stop_retained_variant", "synonymous_variant", + "incomplete_terminal_codon_variant", "coding_sequence_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "coding_transcript_intron_variant", "upstream_gene_variant", "downstream_gene_variant", diff --git a/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml b/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml index ea77fc3dc..1b5097398 100644 --- a/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml +++ b/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml @@ -12423,6 +12423,8 @@ components: - transcript_amplification - feature_elongation - feature_truncation + - inframe_insertion + - inframe_deletion - disruptive_inframe_insertion - disruptive_inframe_deletion - conservative_inframe_insertion @@ -12430,6 +12432,9 @@ components: - missense_variant - rare_amino_acid_variant - protein_altering_variant + - selenocysteine_gain + - selenocysteine_loss + - incomplete_terminal_codon_variant - splice_donor_5th_base_variant - splice_region_variant - exonic_splice_region_variant @@ -12442,10 +12447,13 @@ components: - mature_miRNA_variant - 5_prime_UTR_exon_variant - 5_prime_UTR_intron_variant + - 5_prime_UTR_variant - 3_prime_UTR_exon_variant - 3_prime_UTR_intron_variant + - 3_prime_UTR_variant - non_coding_transcript_exon_variant - non_coding_transcript_intron_variant + - non_coding_transcript_variant - coding_transcript_intron_variant - upstream_gene_variant - downstream_gene_variant @@ -12479,6 +12487,8 @@ components: - transcript_amplification - feature_elongation - feature_truncation + - inframe_insertion + - inframe_deletion - disruptive_inframe_insertion - disruptive_inframe_deletion - conservative_inframe_insertion @@ -12486,6 +12496,9 @@ components: - missense_variant - rare_amino_acid_variant - protein_altering_variant + - selenocysteine_gain + - selenocysteine_loss + - incomplete_terminal_codon_variant - splice_donor_5th_base_variant - splice_region_variant - exonic_splice_region_variant @@ -12498,10 +12511,13 @@ components: - mature_miRNA_variant - 5_prime_UTR_exon_variant - 5_prime_UTR_intron_variant + - 5_prime_UTR_variant - 3_prime_UTR_exon_variant - 3_prime_UTR_intron_variant + - 3_prime_UTR_variant - non_coding_transcript_exon_variant - non_coding_transcript_intron_variant + - non_coding_transcript_variant - coding_transcript_intron_variant - upstream_gene_variant - downstream_gene_variant diff --git a/backend/variants/forms.py b/backend/variants/forms.py index 9fc7ccf63..84279f76c 100644 --- a/backend/variants/forms.py +++ b/backend/variants/forms.py @@ -6,8 +6,10 @@ FILTER_FORM_TRANSLATE_EFFECTS = { "effect_3_prime_UTR_exon_variant": "3_prime_UTR_exon_variant", "effect_3_prime_UTR_intron_variant": "3_prime_UTR_intron_variant", + "effect_3_prime_UTR_variant": "3_prime_UTR_variant", "effect_5_prime_UTR_exon_variant": "5_prime_UTR_exon_variant", "effect_5_prime_UTR_intron_variant": "5_prime_UTR_intron_variant", + "effect_5_prime_UTR_variant": "5_prime_UTR_variant", "effect_coding_sequence_variant": "coding_sequence_variant", "effect_coding_transcript_intron_variant": "coding_transcript_intron_variant", "effect_complex_substitution": "complex_substitution", @@ -25,6 +27,7 @@ "effect_frameshift_truncation": "frameshift_truncation", "effect_frameshift_variant": "frameshift_variant", "effect_gene_variant": "gene_variant", + "effect_incomplete_terminal_codon_variant": "incomplete_terminal_codon_variant", "effect_inframe_deletion": "inframe_deletion", "effect_inframe_insertion": "inframe_insertion", "effect_intergenic_variant": "intergenic_variant", @@ -34,8 +37,11 @@ "effect_mnv": "mnv", "effect_non_coding_transcript_exon_variant": "non_coding_transcript_exon_variant", "effect_non_coding_transcript_intron_variant": "non_coding_transcript_intron_variant", + "effect_non_coding_transcript_variant": "non_coding_transcript_variant", "effect_protein_altering_variant": "protein_altering_variant", "effect_rare_amino_acid_variant": "rare_amino_acid_variant", + "effect_selenocysteine_gain": "selenocysteine_gain", + "effect_selenocysteine_loss": "selenocysteine_loss", "effect_splice_acceptor_variant": "splice_acceptor_variant", "effect_splice_donor_5th_base_variant": "splice_donor_5th_base_variant", "effect_splice_donor_region_variant": "splice_donor_region_variant", diff --git a/backend/variants/query_presets.py b/backend/variants/query_presets.py index 12927ce8e..eb6622917 100644 --- a/backend/variants/query_presets.py +++ b/backend/variants/query_presets.py @@ -611,6 +611,7 @@ class _ImpactPresets: "frameshift_elongation", "frameshift_truncation", "frameshift_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "internal_feature_elongation", @@ -618,6 +619,8 @@ class _ImpactPresets: "mnv", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", @@ -656,6 +659,7 @@ class _ImpactPresets: "frameshift_elongation", "frameshift_truncation", "frameshift_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "internal_feature_elongation", @@ -664,6 +668,8 @@ class _ImpactPresets: "mnv", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", @@ -692,8 +698,10 @@ class _ImpactPresets: "effects": [ "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "complex_substitution", @@ -710,6 +718,7 @@ class _ImpactPresets: "frameshift_elongation", "frameshift_truncation", "frameshift_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "internal_feature_elongation", @@ -718,8 +727,11 @@ class _ImpactPresets: "mnv", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", @@ -749,8 +761,10 @@ class _ImpactPresets: "effects": [ "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "complex_substitution", @@ -768,6 +782,7 @@ class _ImpactPresets: "frameshift_truncation", "frameshift_variant", "gene_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "intergenic_variant", @@ -777,8 +792,11 @@ class _ImpactPresets: "mnv", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", diff --git a/backend/variants/query_schemas.py b/backend/variants/query_schemas.py index 7f4c718ad..0dc499fe0 100644 --- a/backend/variants/query_schemas.py +++ b/backend/variants/query_schemas.py @@ -71,10 +71,12 @@ class Effects(Enum): FEATURE_TRUNCATION = "feature_truncation" FIVE_PRIME_UTR_EXON_VARIANT = "5_prime_UTR_exon_variant" FIVE_PRIME_UTR_INTRON_VARIANT = "5_prime_UTR_intron_variant" + FIVE_PRIME_UTR_VARIANT = "5_prime_UTR_variant" FRAMESHIFT_ELONGATION = "frameshift_elongation" FRAMESHIFT_TRUNCATION = "frameshift_truncation" FRAMESHIFT_VARIANT = "frameshift_variant" GENE_VARIANT = "gene_variant" + INCOMPLETE_TERMINAL_CODON_VARIANT = "incomplete_terminal_codon_variant" INFRAME_DELETION = "inframe_deletion" INFRAME_INSERTION = "inframe_insertion" INTERGENIC_VARIANT = "intergenic_variant" @@ -85,11 +87,14 @@ class Effects(Enum): MNV = "mnv" NON_CODING_TRANSCRIPT_EXON_VARIANT = "non_coding_transcript_exon_variant" NON_CODING_TRANSCRIPT_INTRON_VARIANT = "non_coding_transcript_intron_variant" + NON_CODING_TRANSCRIPT_VARIANT = "non_coding_transcript_variant" PROTEIN_ALTERING_VARIANT = "protein_altering_variant" RARE_AMINO_ACID_VARIANT = "rare_amino_acid_variant" REGULATORY_REGION_ABLATION = "regulatory_region_ablation" REGULATORY_REGION_AMPLIFICATION = "regulatory_region_amplification" REGULATORY_REGION_VARIANT = "regulatory_region_variant" + SELENOCYSTEINE_GAIN = "selenocysteine_gain" + SELENOCYSTEINE_LOSS = "selenocysteine_loss" SPLICE_ACCEPTOR_VARIANT = "splice_acceptor_variant" SPLICE_DONOR_FIFTH_BASE_VARIANT = "splice_donor_5th_base_variant" SPLICE_DONOR_REGION_VARIANT = "splice_donor_region_variant" @@ -108,6 +113,7 @@ class Effects(Enum): TF_BINDING_SITE_VARIANT = "TF_binding_site_variant" THREE_PRIME_UTR_EXON_VARIANT = "3_prime_UTR_exon_variant" THREE_PRIME_UTR_INTRON_VARIANT = "3_prime_UTR_intron_variant" + THREE_PRIME_UTR_VARIANT = "3_prime_UTR_variant" TRANSCRIPT_ABLATION = "transcript_ablation" TRANSCRIPT_AMPLIFICATION = "transcript_amplification" UPSTREAM_GENE_VARIANT = "upstream_gene_variant" diff --git a/backend/variants/schemas/case-query-v1.json b/backend/variants/schemas/case-query-v1.json index 569fce140..2751a9d12 100644 --- a/backend/variants/schemas/case-query-v1.json +++ b/backend/variants/schemas/case-query-v1.json @@ -42,8 +42,10 @@ "enum": [ "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "complex_substitution", @@ -61,6 +63,7 @@ "frameshift_truncation", "frameshift_variant", "gene_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "intergenic_variant", @@ -71,11 +74,14 @@ "mnv", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "protein_altering_variant", "rare_amino_acid_variant", "regulatory_region_ablation", "regulatory_region_amplification", "regulatory_region_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", diff --git a/backend/variants/tests/data/query_settings.py b/backend/variants/tests/data/query_settings.py index 2f9354f6b..ef89c5eaf 100644 --- a/backend/variants/tests/data/query_settings.py +++ b/backend/variants/tests/data/query_settings.py @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:ef62fa8fb86721fee374f48ddea2ccec97b2b4bc08474aa00d987206aa639784 -size 10401 +oid sha256:d056353548116238bb82d715e223cbad2058a228fbc111131550fcbdeac3c131 +size 10671 diff --git a/backend/variants/tests/factories.py b/backend/variants/tests/factories.py index 90f3379f2..0e9bcacd7 100644 --- a/backend/variants/tests/factories.py +++ b/backend/variants/tests/factories.py @@ -155,8 +155,10 @@ class FormDataFactory(FormDataFactoryBase): effect_3_prime_UTR_exon_variant: bool = True effect_3_prime_UTR_intron_variant: bool = True + effect_3_prime_UTR_variant: bool = True effect_5_prime_UTR_exon_variant: bool = True effect_5_prime_UTR_intron_variant: bool = True + effect_5_prime_UTR_variant: bool = True effect_coding_sequence_variant: bool = True effect_coding_transcript_intron_variant: bool = True effect_complex_substitution: bool = True @@ -174,6 +176,7 @@ class FormDataFactory(FormDataFactoryBase): effect_frameshift_truncation: bool = True effect_frameshift_variant: bool = True effect_gene_variant: bool = True + effect_incomplete_terminal_codon_variant: bool = True effect_inframe_deletion: bool = True effect_inframe_insertion: bool = True effect_intergenic_variant: bool = True @@ -183,8 +186,11 @@ class FormDataFactory(FormDataFactoryBase): effect_mnv: bool = True effect_non_coding_transcript_exon_variant: bool = True effect_non_coding_transcript_intron_variant: bool = True + effect_non_coding_transcript_variant: bool = True effect_protein_altering_variant: bool = True effect_rare_amino_acid_variant: bool = True + effect_selenocysteine_gain: bool = True + effect_selenocysteine_loss: bool = True effect_splice_acceptor_variant: bool = True effect_splice_donor_5th_base_variant: bool = True effect_splice_donor_region_variant: bool = True diff --git a/backend/variants/tests/test_queries.py b/backend/variants/tests/test_queries.py index ad4d3c011..35cc6b567 100644 --- a/backend/variants/tests/test_queries.py +++ b/backend/variants/tests/test_queries.py @@ -1843,8 +1843,10 @@ def test_effects_include_missing_annotation(self): "effects": [ "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "complex_substitution", @@ -1862,6 +1864,7 @@ def test_effects_include_missing_annotation(self): "frameshift_truncation", "frameshift_variant", "gene_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "intergenic_variant", @@ -1871,8 +1874,11 @@ def test_effects_include_missing_annotation(self): "mnv", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", diff --git a/backend/variants/tests/test_query_presets.py b/backend/variants/tests/test_query_presets.py index 6ea048618..d2c504637 100644 --- a/backend/variants/tests/test_query_presets.py +++ b/backend/variants/tests/test_query_presets.py @@ -1177,6 +1177,7 @@ def testToSettingsAaChangeSplicing(self): "frameshift_elongation", "frameshift_truncation", "frameshift_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "internal_feature_elongation", @@ -1184,6 +1185,8 @@ def testToSettingsAaChangeSplicing(self): "mnv", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", @@ -1226,6 +1229,7 @@ def testToSettingsAllCodingDeepIntronic(self): "frameshift_elongation", "frameshift_truncation", "frameshift_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "internal_feature_elongation", @@ -1234,6 +1238,8 @@ def testToSettingsAllCodingDeepIntronic(self): "mnv", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", @@ -1266,8 +1272,10 @@ def testToSettingsWholeTranscript(self): "effects": [ "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "complex_substitution", @@ -1284,6 +1292,7 @@ def testToSettingsWholeTranscript(self): "frameshift_elongation", "frameshift_truncation", "frameshift_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "internal_feature_elongation", @@ -1292,8 +1301,11 @@ def testToSettingsWholeTranscript(self): "mnv", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", @@ -1327,8 +1339,10 @@ def testToSettingsAny(self): "effects": [ "3_prime_UTR_exon_variant", "3_prime_UTR_intron_variant", + "3_prime_UTR_variant", "5_prime_UTR_exon_variant", "5_prime_UTR_intron_variant", + "5_prime_UTR_variant", "coding_sequence_variant", "coding_transcript_intron_variant", "complex_substitution", @@ -1346,6 +1360,7 @@ def testToSettingsAny(self): "frameshift_truncation", "frameshift_variant", "gene_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "intergenic_variant", @@ -1355,8 +1370,11 @@ def testToSettingsAny(self): "mnv", "non_coding_transcript_exon_variant", "non_coding_transcript_intron_variant", + "non_coding_transcript_variant", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", @@ -1866,6 +1884,7 @@ def testToSettingsDefaults(self): "frameshift_elongation", "frameshift_truncation", "frameshift_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "internal_feature_elongation", @@ -1873,6 +1892,8 @@ def testToSettingsDefaults(self): "mnv", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", diff --git a/backend/variants/tests/test_ui.py b/backend/variants/tests/test_ui.py index 4167b172a..5ca2d2796 100644 --- a/backend/variants/tests/test_ui.py +++ b/backend/variants/tests/test_ui.py @@ -193,8 +193,10 @@ def assert_element_exists(self, kwargs, element_id, exists): EFFECT_FIELDS = { "id_effect_3_prime_UTR_exon_variant": False, "id_effect_3_prime_UTR_intron_variant": False, + "id_effect_3_prime_UTR_variant": False, "id_effect_5_prime_UTR_exon_variant": False, "id_effect_5_prime_UTR_intron_variant": False, + "id_effect_5_prime_UTR_variant": False, "id_effect_coding_sequence_variant": False, "id_effect_coding_transcript_intron_variant": False, "id_effect_complex_substitution": False, @@ -212,6 +214,7 @@ def assert_element_exists(self, kwargs, element_id, exists): "id_effect_frameshift_truncation": False, "id_effect_frameshift_variant": False, "id_effect_gene_variant": False, + "id_effect_incomplete_terminal_codon_variant": False, "id_effect_inframe_deletion": False, "id_effect_inframe_insertion": False, "id_effect_intergenic_variant": False, @@ -221,8 +224,11 @@ def assert_element_exists(self, kwargs, element_id, exists): "id_effect_mnv": False, "id_effect_non_coding_transcript_exon_variant": False, "id_effect_non_coding_transcript_intron_variant": False, + "id_effect_non_coding_transcript_variant": False, "id_effect_protein_altering_variant": False, "id_effect_rare_amino_acid_variant": False, + "id_effect_selenocysteine_gain": False, + "id_effect_selenocysteine_loss": False, "id_effect_splice_acceptor_variant": False, "id_effect_splice_donor_5th_base_variant": False, "id_effect_splice_donor_region_variant": False, diff --git a/backend/variants/tests/test_views_api.py b/backend/variants/tests/test_views_api.py index 1bbb1d93f..45526a54a 100644 --- a/backend/variants/tests/test_views_api.py +++ b/backend/variants/tests/test_views_api.py @@ -711,6 +711,7 @@ def test_get_success(self): "frameshift_elongation", "frameshift_truncation", "frameshift_variant", + "incomplete_terminal_codon_variant", "inframe_deletion", "inframe_insertion", "internal_feature_elongation", @@ -718,6 +719,8 @@ def test_get_success(self): "mnv", "protein_altering_variant", "rare_amino_acid_variant", + "selenocysteine_gain", + "selenocysteine_loss", "splice_acceptor_variant", "splice_donor_5th_base_variant", "splice_donor_region_variant", diff --git a/frontend/ext/varfish-api/src/lib/types.gen.ts b/frontend/ext/varfish-api/src/lib/types.gen.ts index 9c3f4ed3e..8249514d5 100644 --- a/frontend/ext/varfish-api/src/lib/types.gen.ts +++ b/frontend/ext/varfish-api/src/lib/types.gen.ts @@ -3149,9 +3149,9 @@ export type SeqvarsVariantAnnotationPydantic = { /** * The variant consequence. */ -export type SeqvarsVariantConsequenceChoice = 'transcript_ablation' | 'exon_loss_variant' | 'splice_acceptor_variant' | 'splice_donor_variant' | 'stop_gained' | 'frameshift_variant' | 'stop_lost' | 'start_lost' | 'transcript_amplification' | 'feature_elongation' | 'feature_truncation' | 'disruptive_inframe_insertion' | 'disruptive_inframe_deletion' | 'conservative_inframe_insertion' | 'conservative_inframe_deletion' | 'missense_variant' | 'splice_donor_5th_base_variant' | 'splice_region_variant' | 'splice_donor_region_variant' | 'splice_polypyrimidine_tract_variant' | 'start_retained_variant' | 'stop_retained_variant' | 'synonymous_variant' | 'coding_sequence_variant' | 'mature_miRNA_variant' | '5_prime_UTR_exon_variant' | '5_prime_UTR_intron_variant' | '3_prime_UTR_exon_variant' | '3_prime_UTR_intron_variant' | 'non_coding_transcript_exon_variant' | 'non_coding_transcript_intron_variant' | 'coding_transcript_intron_variant' | 'upstream_gene_variant' | 'downstream_gene_variant' | 'TFBS_ablation' | 'TFBS_amplification' | 'TF_binding_site_variant' | 'regulatory_region_ablation' | 'regulatory_region_amplification' | 'regulatory_region_variant' | 'intergenic_variant' | 'intron_variant' | 'gene_variant' | 'protein_altering_variant' | 'frameshift_elongation' | 'frameshift_truncation' | 'rare_amino_acid_variant' | 'exonic_splice_region_variant'; +export type SeqvarsVariantConsequenceChoice = 'transcript_ablation' | 'exon_loss_variant' | 'splice_acceptor_variant' | 'splice_donor_variant' | 'stop_gained' | 'frameshift_variant' | 'stop_lost' | 'start_lost' | 'transcript_amplification' | 'feature_elongation' | 'feature_truncation' | 'disruptive_inframe_insertion' | 'disruptive_inframe_deletion' | 'conservative_inframe_insertion' | 'conservative_inframe_deletion' | 'missense_variant' | 'splice_donor_5th_base_variant' | 'splice_region_variant' | 'splice_donor_region_variant' | 'splice_polypyrimidine_tract_variant' | 'start_retained_variant' | 'stop_retained_variant' | 'synonymous_variant' | 'coding_sequence_variant' | 'mature_miRNA_variant' | '5_prime_UTR_exon_variant' | '5_prime_UTR_intron_variant' | '5_prime_UTR_variant' | '3_prime_UTR_exon_variant' | '3_prime_UTR_intron_variant' | '3_prime_UTR_variant' | 'non_coding_transcript_exon_variant' | 'non_coding_transcript_intron_variant' | 'non_coding_transcript_variant' | 'coding_transcript_intron_variant' | 'upstream_gene_variant' | 'downstream_gene_variant' | 'TFBS_ablation' | 'TFBS_amplification' | 'TF_binding_site_variant' | 'regulatory_region_ablation' | 'regulatory_region_amplification' | 'regulatory_region_variant' | 'intergenic_variant' | 'intron_variant' | 'gene_variant' | 'protein_altering_variant' | 'frameshift_elongation' | 'frameshift_truncation' | 'rare_amino_acid_variant' | 'exonic_splice_region_variant' | 'inframe_deletion' | 'inframe_insertion' | 'selenocysteine_gain' | 'selenocysteine_loss' | 'incomplete_terminal_codon_variant'; -export type SeqvarsVariantConsequenceChoiceList = Array<('transcript_ablation' | 'exon_loss_variant' | 'splice_acceptor_variant' | 'splice_donor_variant' | 'stop_gained' | 'frameshift_variant' | 'stop_lost' | 'start_lost' | 'transcript_amplification' | 'feature_elongation' | 'feature_truncation' | 'disruptive_inframe_insertion' | 'disruptive_inframe_deletion' | 'conservative_inframe_insertion' | 'conservative_inframe_deletion' | 'missense_variant' | 'splice_donor_5th_base_variant' | 'splice_region_variant' | 'splice_donor_region_variant' | 'splice_polypyrimidine_tract_variant' | 'start_retained_variant' | 'stop_retained_variant' | 'synonymous_variant' | 'coding_sequence_variant' | 'mature_miRNA_variant' | '5_prime_UTR_exon_variant' | '5_prime_UTR_intron_variant' | '3_prime_UTR_exon_variant' | '3_prime_UTR_intron_variant' | 'non_coding_transcript_exon_variant' | 'non_coding_transcript_intron_variant' | 'coding_transcript_intron_variant' | 'upstream_gene_variant' | 'downstream_gene_variant' | 'TFBS_ablation' | 'TFBS_amplification' | 'TF_binding_site_variant' | 'regulatory_region_ablation' | 'regulatory_region_amplification' | 'regulatory_region_variant' | 'intergenic_variant' | 'intron_variant' | 'gene_variant' | 'protein_altering_variant' | 'frameshift_elongation' | 'frameshift_truncation' | 'rare_amino_acid_variant' | 'exonic_splice_region_variant')>; +export type SeqvarsVariantConsequenceChoiceList = Array<('transcript_ablation' | 'exon_loss_variant' | 'splice_acceptor_variant' | 'splice_donor_variant' | 'stop_gained' | 'frameshift_variant' | 'stop_lost' | 'start_lost' | 'transcript_amplification' | 'feature_elongation' | 'feature_truncation' | 'disruptive_inframe_insertion' | 'disruptive_inframe_deletion' | 'conservative_inframe_insertion' | 'conservative_inframe_deletion' | 'missense_variant' | 'splice_donor_5th_base_variant' | 'splice_region_variant' | 'splice_donor_region_variant' | 'splice_polypyrimidine_tract_variant' | 'start_retained_variant' | 'stop_retained_variant' | 'synonymous_variant' | 'coding_sequence_variant' | 'mature_miRNA_variant' | '5_prime_UTR_exon_variant' | '5_prime_UTR_intron_variant' | '5_prime_UTR_variant' | '3_prime_UTR_exon_variant' | '3_prime_UTR_intron_variant' | '3_prime_UTR_variant' | 'non_coding_transcript_exon_variant' | 'non_coding_transcript_intron_variant' | 'non_coding_transcript_variant' | 'coding_transcript_intron_variant' | 'upstream_gene_variant' | 'downstream_gene_variant' | 'TFBS_ablation' | 'TFBS_amplification' | 'TF_binding_site_variant' | 'regulatory_region_ablation' | 'regulatory_region_amplification' | 'regulatory_region_variant' | 'intergenic_variant' | 'intron_variant' | 'gene_variant' | 'protein_altering_variant' | 'frameshift_elongation' | 'frameshift_truncation' | 'rare_amino_acid_variant' | 'exonic_splice_region_variant' | 'inframe_deletion' | 'inframe_insertion' | 'selenocysteine_gain' | 'selenocysteine_loss' | 'incomplete_terminal_codon_variant')>; /** * Store variant-related annotation. diff --git a/frontend/src/seqvars/components/PresetsEditor/lib/consequence.ts b/frontend/src/seqvars/components/PresetsEditor/lib/consequence.ts index c8252206c..8ca2e4714 100644 --- a/frontend/src/seqvars/components/PresetsEditor/lib/consequence.ts +++ b/frontend/src/seqvars/components/PresetsEditor/lib/consequence.ts @@ -72,6 +72,14 @@ export const CODING_CONSEQUENCES: ConsequenceChoice[] = [ label: 'coding transcript intron', key: 'coding_transcript_intron_variant', }, + { label: 'inframe deletion', key: 'inframe_deletion' }, + { label: 'inframe insertion', key: 'inframe_insertion' }, + { + label: 'incomplete terminal codon', + key: 'incomplete_terminal_codon_variant', + }, + { label: 'selenocysteine gain', key: 'selenocysteine_gain' }, + { label: 'selenocysteine loss', key: 'selenocysteine_loss' }, ] as const /** Consequence choices in "off-exomes" category. */ @@ -86,10 +94,13 @@ export const OFF_EXOMES_CONSEQUENCES: ConsequenceChoice[] = [ export const NON_CODING_CONSEQUENCES: ConsequenceChoice[] = [ { label: "5' UTR exon variant", key: '5_prime_UTR_exon_variant' }, { label: "5' UTR intron variant", key: '5_prime_UTR_intron_variant' }, + { label: "5' UTR variant", key: '5_prime_UTR_variant' }, { label: "3' UTR exon variant", key: '3_prime_UTR_exon_variant' }, + { label: "3' UTR variant", key: '3_prime_UTR_variant' }, { label: "3' UTR intron variant", key: '3_prime_UTR_intron_variant' }, { label: 'non-coding exonic', key: 'non_coding_transcript_exon_variant' }, { label: 'non-coding intronic', key: 'non_coding_transcript_intron_variant' }, + { label: 'non-coding transcript', key: 'non_coding_transcript_variant' }, ] as const /** Consequence choices in "splicing" category. */ @@ -137,6 +148,10 @@ export const CONSEQUENCE_GROUP_INFOS: ConsequenceGroupInfo[] = [ 'feature_truncation', 'frameshift_elongation', 'frameshift_truncation', + 'inframe_deletion', + 'inframe_insertion', + 'selenocysteine_gain', + 'selenocysteine_loss', ], }, { @@ -173,6 +188,11 @@ export const CONSEQUENCE_GROUP_INFOS: ConsequenceGroupInfo[] = [ 'synonymous_variant', 'protein_altering_variant', 'rare_amino_acid_variant', + 'inframe_deletion', + 'inframe_insertion', + 'incomplete_terminal_codon_variant', + 'selenocysteine_gain', + 'selenocysteine_loss', ], }, { @@ -181,8 +201,10 @@ export const CONSEQUENCE_GROUP_INFOS: ConsequenceGroupInfo[] = [ valueKeys: [ '5_prime_UTR_exon_variant', '5_prime_UTR_intron_variant', + '5_prime_UTR_variant', '3_prime_UTR_exon_variant', '3_prime_UTR_intron_variant', + '3_prime_UTR_variant', ], }, { @@ -199,8 +221,15 @@ export const CONSEQUENCE_GROUP_INFOS: ConsequenceGroupInfo[] = [ label: 'non-coding', key: ConsequenceGroup.NON_CODING, valueKeys: [ + '5_prime_UTR_exon_variant', + '5_prime_UTR_intron_variant', + '5_prime_UTR_variant', + '3_prime_UTR_exon_variant', + '3_prime_UTR_intron_variant', + '3_prime_UTR_variant', 'non_coding_transcript_exon_variant', 'non_coding_transcript_intron_variant', + 'non_coding_transcript_variant', ], }, { diff --git a/frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue b/frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue index c1b9dd9b4..def91f515 100644 --- a/frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue +++ b/frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue @@ -96,10 +96,13 @@ const CONSEQUENCE_LABEL: Record = { mature_miRNA_variant: 'mature miRNA', '5_prime_UTR_exon_variant': "5' UTR exon", '5_prime_UTR_intron_variant': "5' UTR intron", + '5_prime_UTR_variant': "5' UTR", '3_prime_UTR_exon_variant': "3' UTR exon", '3_prime_UTR_intron_variant': "3' UTR intron", + '3_prime_UTR_variant': "3' UTR", non_coding_transcript_exon_variant: 'nc tx exon', non_coding_transcript_intron_variant: 'nc tx intron', + non_coding_transcript_variant: 'nc tx', coding_transcript_intron_variant: 'coding tx intron', upstream_gene_variant: 'upstream', downstream_gene_variant: 'downstream', @@ -112,6 +115,11 @@ const CONSEQUENCE_LABEL: Record = { intergenic_variant: 'intergenic', intron_variant: 'intronic', gene_variant: 'gene variant', + selenocysteine_gain: 'selenocysteine gain', + selenocysteine_loss: 'selenocysteine loss', + inframe_deletion: 'inframe deletion', + inframe_insertion: 'inframe insertion', + incomplete_terminal_codon_variant: 'incomplete terminal codon', } /** Review status labels. */ diff --git a/frontend/src/variants/components/FilterForm/EffectPane.fields.js b/frontend/src/variants/components/FilterForm/EffectPane.fields.js index 6e8585650..ae0014876 100644 --- a/frontend/src/variants/components/FilterForm/EffectPane.fields.js +++ b/frontend/src/variants/components/FilterForm/EffectPane.fields.js @@ -73,6 +73,13 @@ export const detailedEffectGroups = Object.freeze([ explanation: 'A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.', }, + { + id: 'incomplete_terminal_codon_variant', + label: 'incomplete terminal codon', + so: 'SO:0001626', + explanation: + 'A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.', + }, { id: 'inframe_deletion', label: 'inframe deletion', @@ -108,6 +115,20 @@ export const detailedEffectGroups = Object.freeze([ explanation: 'An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence.', }, + { + id: 'selenocysteine_gain', + label: 'selenocysteine gain', + so: 'SO:selenocysteine_gain', + explanation: + 'A sequence variant whereby at least one base of a codon is changed, resulting in a selenocysteine.', + }, + { + id: 'selenocysteine_loss', + label: 'selenocysteine loss', + so: 'SO:selenocysteine_loss', + explanation: + 'A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid.', + }, { id: 'start_lost', label: 'start lost', @@ -259,6 +280,12 @@ export const detailedEffectGroups = Object.freeze([ so: 'SO:0002090', explanation: "An intron UTR variant between 3' UTRs.", }, + { + id: '3_prime_UTR_variant', + label: "3' UTR variant", + so: 'SO:0001624', + explanation: "A UTR variant of the 3' UTR.", + }, { id: '5_prime_UTR_exon_variant', label: "5' UTR exonic", @@ -271,6 +298,12 @@ export const detailedEffectGroups = Object.freeze([ so: 'SO:0002091', explanation: "An intron UTR variant between 5' UTRs.", }, + { + id: '5_prime_UTR_variant', + label: "5' UTR variant", + so: 'SO:0001623', + explanation: "A UTR variant of the 5' UTR.", + }, { id: 'non_coding_transcript_exon_variant', label: 'n.c. exonic', @@ -285,6 +318,12 @@ export const detailedEffectGroups = Object.freeze([ explanation: 'A transcript variant occurring within an intron of a non coding transcript.', }, + { + id: 'non_coding_transcript_variant', + label: 'n.c. transcript', + so: 'SO:0001619', + explanation: 'A transcript variant of a non coding RNA gene.', + }, { id: 'gene_variant', label: 'gene variant', @@ -404,6 +443,8 @@ const _effectGroups = { 'missense_variant', 'mnv', 'protein_altering_variant', + 'selenocysteine_gain', + 'selenocysteine_loss', 'start_lost', 'stop_gained', 'stop_lost', @@ -426,8 +467,13 @@ const _effectGroups = { 'conservative_inframe_deletion', 'conservative_inframe_insertion', 'exonic_splice_region_variant', + 'incomplete_terminal_codon_variant', + 'inframe_deletion', + 'inframe_insertion', 'protein_altering_variant', 'rare_amino_acid_variant', + 'selenocysteine_gain', + 'selenocysteine_loss', 'start_retained_variant', 'stop_retained_variant', 'synonymous_variant', @@ -435,17 +481,26 @@ const _effectGroups = { utr_intronic: [ '3_prime_UTR_exon_variant', '3_prime_UTR_intron_variant', + '3_prime_UTR_variant', '5_prime_UTR_exon_variant', '5_prime_UTR_intron_variant', + '5_prime_UTR_variant', 'coding_transcript_intron_variant', 'intron_variant', ], noncoding: [ + '3_prime_UTR_exon_variant', + '3_prime_UTR_intron_variant', + '3_prime_UTR_variant', + '5_prime_UTR_exon_variant', + '5_prime_UTR_intron_variant', + '5_prime_UTR_variant', 'downstream_gene_variant', 'gene_variant', 'intergenic_variant', 'non_coding_transcript_exon_variant', 'non_coding_transcript_intron_variant', + 'non_coding_transcript_variant', 'upstream_gene_variant', ], nonsense: [ diff --git a/frontend/tests/variants/unit/components/FilterForm/EffectPane.spec.js b/frontend/tests/variants/unit/components/FilterForm/EffectPane.spec.js index bf66b6abf..9efc47cf5 100644 --- a/frontend/tests/variants/unit/components/FilterForm/EffectPane.spec.js +++ b/frontend/tests/variants/unit/components/FilterForm/EffectPane.spec.js @@ -15,7 +15,8 @@ describe('FilterFormEffectPane.vue', () => { }, }) - expect(wrapper.findAll('input').length).toBe(61) + // 66 effect checkbox inputs (detailedEffectGroups) + 1 maxExonDist text input + expect(wrapper.findAll('input').length).toBe(67) expect(wrapper.findAll('.alert-secondary').length).toBe(6) })