cool_seq_tool.schemas

Defines attribute constants, useful object structures, and API response schemas.

class cool_seq_tool.schemas.AnnotationLayer(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Create enum for supported annotation layers

CDNA = 'c'

GENOMIC = 'g'

PROTEIN = 'p'

class cool_seq_tool.schemas.Assembly(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Define supported genomic assemblies. Must be defined in ascending order

GRCH37 = 'GRCh37'

GRCH38 = 'GRCh38'

classmethod values()

Return list of values in enum (ascending assembly order)

Return type:

list[str]

class cool_seq_tool.schemas.BaseModelForbidExtra(**data)

Base Pydantic model class with extra values forbidden.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

class cool_seq_tool.schemas.CoordinateType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Create Enum for coordinate types.

It is preferred to operate in inter-residue coordinates, but users should be careful to define the coordinate mode of their data when calling cool-seq-tool functions.

RESIDUE means 1-indexed, residue coordinates and INTER_RESIDUE means 0-indexed, inter-residue coordinates.

		C		T		G
RESIDUE		1		2		3
INTER_RESIDUE	0		1		2		3

See “Conventions that promote reliable data sharing” and figure 3 within the Variation Representation Schema (VRS) paper for further discussion.

INTER_RESIDUE = 'inter-residue'

RESIDUE = 'residue'

class cool_seq_tool.schemas.GenomicTxData(**data)

Represent aligned genomic/transcript exon data

alt_aln_method: str

alt_exon_id: int

alt_pos_range: tuple[int, int]

gene: str

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

strand: Strand

tx_exon_id: int

tx_pos_range: tuple[int, int]

class cool_seq_tool.schemas.GenomicTxMetadata(**data)

Store relevant metadata for genomic and transcript accessions

alt_ac: str

alt_pos_change_range: tuple[int, int]

coding_end_site: int

coding_start_site: int

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

pos_change: Optional[tuple[int, int]]

tx_ac: str

class cool_seq_tool.schemas.ManeGeneData(**data)

Define minimal object model for representing a MANE gene

hgnc_id: Optional[Annotated[int]]

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

ncbi_gene_id: Annotated[int]

symbol: Annotated[str]

class cool_seq_tool.schemas.ServiceMeta(**data)

Metadata for cool_seq_tool service

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

name: Literal['cool_seq_tool']

response_datetime: datetime

url: Literal['https://github.com/GenomicMedLab/cool-seq-tool']

version: Annotated[str]

class cool_seq_tool.schemas.Strand(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Create enum for positive and negative strand

NEGATIVE = -1

POSITIVE = 1

class cool_seq_tool.schemas.TranscriptPriority(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Create Enum for Transcript Priority labels

GRCH38 = 'grch38'

LONGEST_COMPATIBLE_REMAINING = 'longest_compatible_remaining'

MANE_PLUS_CLINICAL = 'mane_plus_clinical'

MANE_SELECT = 'mane_select'