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)[source]#

Create enum for supported annotation layers

CDNA = 'c'[source]#

GENOMIC = 'g'[source]#

PROTEIN = 'p'[source]#

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

Define supported genomic assemblies. Must be defined in ascending order

GRCH37 = 'GRCh37'[source]#

GRCH38 = 'GRCh38'[source]#

classmethod values()[source]#

Return list of values in enum (ascending assembly order)

Return type:: list[str]

class cool_seq_tool.schemas.BaseModelForbidExtra(**data)[source]#: Base Pydantic model class with extra values forbidden.

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

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'[source]#

RESIDUE = 'residue'[source]#

class cool_seq_tool.schemas.GenomicTxData(**data)[source]#

Represent aligned genomic/transcript exon data

alt_aln_method: str[source]#

alt_exon_id: int[source]#

alt_pos_range: tuple[int, int][source]#

gene: str[source]#

strand: Strand[source]#

tx_exon_id: int[source]#

tx_pos_range: tuple[int, int][source]#

class cool_seq_tool.schemas.GenomicTxMetadata(**data)[source]#

Store relevant metadata for genomic and transcript accessions

alt_ac: str[source]#

alt_pos_change_range: tuple[int, int][source]#

coding_end_site: int[source]#

coding_start_site: int[source]#

pos_change: Optional[tuple[int, int]][source]#

tx_ac: str[source]#

class cool_seq_tool.schemas.ManeGeneData(**data)[source]#

Define minimal object model for representing a MANE gene

hgnc_id: Optional[Annotated[int]][source]#

ncbi_gene_id: Annotated[int][source]#

status: list[ManeStatus][source]#

symbol: Annotated[str][source]#

class cool_seq_tool.schemas.ManeStatus(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Define constraints for mane status

PLUS_CLINICAL = 'mane_plus_clinical'[source]#

SELECT = 'mane_select'[source]#

class cool_seq_tool.schemas.ServiceMeta(**data)[source]#

Metadata for cool_seq_tool service

name: Literal['cool_seq_tool'][source]#

response_datetime: datetime[source]#

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

version: Annotated[str][source]#

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

Create enum for positive and negative strand

NEGATIVE = -1[source]#

POSITIVE = 1[source]#

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

Create Enum for Transcript Priority labels

GRCH38 = 'grch38'[source]#

LONGEST_COMPATIBLE_REMAINING = 'longest_compatible_remaining'[source]#

MANE_PLUS_CLINICAL = 'mane_plus_clinical'[source]#

MANE_SELECT = 'mane_select'[source]#