openapi: 3.0.3
info:
title: mehari
description: Variant effect prediction all in Rust
contact:
name: Manuel Holtgrewe
email: manuel.holtgrewe@bih-charite.de
license:
name: MIT
version: 0.29.6
paths:
/api/v1/seqvars/csq:
get:
tags:
- seqvars_csq
summary: Query for consequence of a variant.
operationId: seqvarsCsq
parameters:
- name: genome_release
in: query
description: The assembly.
required: true
schema:
$ref: '#/components/schemas/GenomeRelease'
- name: chromosome
in: query
description: SPDI sequence.
required: true
schema:
type: string
- name: position
in: query
description: SPDI position.
required: true
schema:
type: integer
format: int32
minimum: 0
- name: reference
in: query
description: SPDI deletion.
required: true
schema:
type: string
- name: alternative
in: query
description: SPDI insertion.
required: true
schema:
type: string
- name: hgnc_id
in: query
description: Optionally, the HGNC ID of the gene to limit to.
required: false
schema:
type: string
nullable: true
responses:
'200':
description: Seqvars consequence information.
content:
application/json:
schema:
$ref: '#/components/schemas/SeqvarsCsqResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/strucvars/csq:
get:
tags:
- strucvars_csq
summary: Query for consequence of a variant.
operationId: strucvarsCsq
parameters:
- name: genome_release
in: query
description: The assembly.
required: true
schema:
$ref: '#/components/schemas/GenomeRelease'
- name: chromosome
in: query
description: Chromosome.
required: true
schema:
type: string
- name: start
in: query
description: 1-based start position.
required: true
schema:
type: integer
format: int32
- name: stop
in: query
description: 1-based stop position, ignored for INS.
required: false
schema:
type: integer
format: int32
nullable: true
- name: sv_type
in: query
description: The variant type to use for annotation.
required: true
schema:
$ref: '#/components/schemas/StrucvarsSvType'
responses:
'200':
description: Strucvars consequence information.
content:
application/json:
schema:
$ref: '#/components/schemas/StrucvarsCsqResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/versionsInfo:
get:
tags:
- versions
summary: Query for consequence of a variant.
operationId: versionsInfo
responses:
'200':
description: Version information.
content:
application/json:
schema:
$ref: '#/components/schemas/VersionsInfoResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
components:
schemas:
Assembly:
type: string
description: |-
Assembly to be passed on the command line.
Copy from annonars with extension to derive `utoipa::ToSchema`.
enum:
- grch37
- grch38
Consequence:
type: string
description: Putative impact.
enum:
- 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
- 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
CustomError:
type: object
required:
- err
properties:
err:
type: string
DataVersionEntry:
type: object
description: Specification of data version for a given genome build.
required:
- genome_build
- version_cdot
properties:
genome_build:
$ref: '#/components/schemas/Assembly'
version_refseq:
type: string
description: Version of the RefSeq database, if any.
nullable: true
version_ensembl:
type: string
description: Version of the Ensembl database, if any.
nullable: true
version_cdot:
type: string
description: Version of cdot used.
FeatureBiotype:
type: string
description: Encode feature biotype.
enum:
- coding
- noncoding
- mane_select
- mane_plus_clinical
FeatureType:
oneOf:
- type: object
required:
- so_term
properties:
so_term:
type: object
required:
- term
properties:
term:
$ref: '#/components/schemas/SoFeature'
- type: object
required:
- custom
properties:
custom:
type: object
required:
- value
properties:
value:
type: string
description: Enum for `AnnField::feature_type`.
GenomeRelease:
type: string
description: Select the genome release to use.
enum:
- grch37
- grch38
Message:
type: string
description: A message to be used in `AnnField::messages`.
enum:
- error_chromosome_not_found
- error_out_of_chromosome_range
- warning_ref_does_not_match_genome
- warning_sequence_not_available
- warning_transcript_incomplete
- warning_transcript_multiple_stop_codons
- warning_transcripts_no_start_codon
- info_realign_three_prime
- info_compound_annotation
- info_non_reference_annotation
Pos:
type: object
description: Position, optionally with total length.
required:
- ord
properties:
ord:
type: integer
format: int32
total:
type: integer
format: int32
nullable: true
PutativeImpact:
type: string
description: Putative impact level.
enum:
- high
- moderate
- low
- modifier
Rank:
type: object
description: Encode exon/intron rank.
required:
- ord
- total
properties:
ord:
type: integer
format: int32
total:
type: integer
format: int32
SeqvarsCsqQuery:
type: object
description: Query parameters of the `/api/v1/seqvars/csq` endpoint.
required:
- genome_release
- chromosome
- position
- reference
- alternative
properties:
genome_release:
$ref: '#/components/schemas/GenomeRelease'
chromosome:
type: string
description: SPDI sequence.
position:
type: integer
format: int32
description: SPDI position.
minimum: 0
reference:
type: string
description: SPDI deletion.
alternative:
type: string
description: SPDI insertion.
hgnc_id:
type: string
description: Optionally, the HGNC ID of the gene to limit to.
nullable: true
SeqvarsCsqResponse:
type: object
description: Response of the `/api/v1/seqvars/csq` endpoint.
required:
- version
- query
- result
properties:
version:
$ref: '#/components/schemas/VersionsInfoResponse'
query:
$ref: '#/components/schemas/SeqvarsCsqQuery'
result:
type: array
items:
$ref: '#/components/schemas/SeqvarsCsqResultEntry'
description: The resulting records for the scored genes.
SeqvarsCsqResultEntry:
type: object
description: One entry in `SeqvarsCsqResponse`.
required:
- consequences
- putative_impact
- gene_symbol
- gene_id
- feature_type
- feature_id
- feature_biotype
- feature_tag
properties:
consequences:
type: array
items:
$ref: '#/components/schemas/Consequence'
description: The consequences of the allele.
putative_impact:
$ref: '#/components/schemas/PutativeImpact'
gene_symbol:
type: string
description: The gene symbol.
gene_id:
type: string
description: The gene identifier.
feature_type:
$ref: '#/components/schemas/FeatureType'
feature_id:
type: string
description: The feature identifier.
feature_biotype:
$ref: '#/components/schemas/FeatureBiotype'
feature_tag:
type: array
items:
$ref: '#/components/schemas/FeatureBiotype'
description: The feature tags.
rank:
allOf:
- $ref: '#/components/schemas/Rank'
nullable: true
hgvs_t:
type: string
description: HGVS c. notation.
nullable: true
hgvs_p:
type: string
description: HGVS p. notation.
nullable: true
tx_pos:
allOf:
- $ref: '#/components/schemas/Pos'
nullable: true
cds_pos:
allOf:
- $ref: '#/components/schemas/Pos'
nullable: true
protein_pos:
allOf:
- $ref: '#/components/schemas/Pos'
nullable: true
distance:
type: integer
format: int32
description: Distance to feature.
nullable: true
messages:
type: array
items:
$ref: '#/components/schemas/Message'
description: Optional list of warnings and error messages.
nullable: true
SoFeature:
type: string
description: Sequence ontology feature.
enum:
- Transcript
SoftwareVersions:
type: object
description: Software version specification.
required:
- mehari
- hgvs_rs
properties:
mehari:
type: string
description: Version of `mehari`.
hgvs_rs:
type: string
description: Version of the `hgvs` crate.
StrucvarsCsqQuery:
type: object
description: Query parameters of the `/api/v1/strucvars/csq` endpoint.
required:
- genome_release
- chromosome
- start
- sv_type
properties:
genome_release:
$ref: '#/components/schemas/GenomeRelease'
chromosome:
type: string
description: Chromosome.
start:
type: integer
format: int32
description: 1-based start position.
stop:
type: integer
format: int32
description: 1-based stop position, ignored for INS.
nullable: true
sv_type:
$ref: '#/components/schemas/StrucvarsSvType'
StrucvarsCsqResponse:
type: object
description: Response of the `/api/v1/strucvars/csq` endpoint.
required:
- version
- query
- result
properties:
version:
$ref: '#/components/schemas/VersionsInfoResponse'
query:
$ref: '#/components/schemas/StrucvarsCsqQuery'
result:
type: array
items:
$ref: '#/components/schemas/StrucvarsGeneTranscriptEffects'
description: The resulting records for the affected genes.
StrucvarsGeneTranscriptEffects:
type: object
description: Explanation of transcript effect per individual gene.
required:
- hgnc_id
- transcript_effects
properties:
hgnc_id:
type: string
description: HGNC identifier
transcript_effects:
type: array
items:
$ref: '#/components/schemas/StrucvarsTranscriptEffect'
description: Transcript effects for the gene.
StrucvarsSvType:
type: string
description: Structural Variant type.
enum:
- DEL
- DUP
- INS
- INV
- BND
StrucvarsTranscriptEffect:
type: string
description: Enumeration for effect on transcript.
enum:
- transcript_variant
- exon_variant
- splice_region_variant
- intron_variant
- upstream_variant
- downstream_variant
- intergenic_variant
VersionsInfoResponse:
type: object
description: Response of the `/api/v1/version` endpoint.
required:
- software
- data
properties:
software:
$ref: '#/components/schemas/SoftwareVersions'
data:
type: array
items:
$ref: '#/components/schemas/DataVersionEntry'
description: Data versions specification.