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: Literal['c'] = 'c'

GENOMIC: Literal['g'] = 'g'

PROTEIN: Literal['p'] = '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.CdnaRepresentation(**data)

Model response for cDNA representation

c_ac: Annotated[str]

c_end_pos: Annotated[int]

c_start_pos: Annotated[int]

cds_start: Annotated[int]

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

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

residue_mode: Literal[<ResidueMode.INTER_RESIDUE: 'inter-residue'>]

class cool_seq_tool.schemas.GenomicData(**data)

Model containing genomic and transcript exon data.

classmethod check_start_end(values)

Check that at least one of {start, end} is set. Check that at least one of {exon_start, exon_end} is set. If not set, set corresponding offset to None

chr: Annotated[str]

end: Optional[Annotated[int]]

exon_end: Optional[Annotated[int]]

exon_end_offset: Optional[Annotated[int]]

exon_start: Optional[Annotated[int]]

exon_start_offset: Optional[Annotated[int]]

gene: Annotated[str]

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

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

start: Optional[Annotated[int]]

strand: Strand

transcript: Annotated[str]

class cool_seq_tool.schemas.GenomicDataResponse(**data)

Response model for Genomic Data

genomic_data: Optional[GenomicData]

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

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

service_meta: ServiceMeta

warnings: list[Annotated[str]]

class cool_seq_tool.schemas.GenomicRepresentation(**data)

Model response for genomic representation

g_ac: str

g_end_pos: int

g_start_pos: int

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

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

residue_mode: Literal[<ResidueMode.INTER_RESIDUE: 'inter-residue'>]

class cool_seq_tool.schemas.GenomicRequestBody(**data)

Define constraints for genomic to transcript exon coordinates request body

classmethod check_start_and_end(values)

Check that at least one of {start, end} is set

chromosome: Union[Annotated[str], Annotated[int]]

end: Optional[Annotated[int]]

gene: Optional[Annotated[str]]

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

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

residue_mode: ResidueMode

start: Optional[Annotated[int]]

strand: Optional[Strand]

transcript: Optional[Annotated[str]]

class cool_seq_tool.schemas.ManeData(**data)

Define mane data fields

ensembl: Optional[Annotated[str]]

gene: Optional[Annotated[str]]

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

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

pos: tuple[int, int]

refseq: Optional[Annotated[str]]

status: TranscriptPriority

strand: Strand

class cool_seq_tool.schemas.ManeDataService(**data)

Service model response for getting mane data

mane_data: Optional[ManeData]

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

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

service_meta: ServiceMeta

warnings: list[Annotated[str]]

class cool_seq_tool.schemas.MappedManeData(**data)

Define mapped mane data fields

alt_ac: Annotated[str]

assembly: Assembly

ensembl: Optional[Annotated[str]]

gene: Annotated[str]

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

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

refseq: Annotated[str]

status: TranscriptPriority

strand: Strand

class cool_seq_tool.schemas.MappedManeDataService(**data)

Service model response for mapped mane data

mapped_mane_data: Optional[MappedManeData]

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

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

service_meta: ServiceMeta

warnings: list[Annotated[str]]

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

Create Enum for residue modes.

We typically prefer 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.

		C		T		G
ZERO		0		1		2
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'

ZERO = 'zero'

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.ToCdnaService(**data)

Service model response for protein -> cDNA

c_data: Optional[CdnaRepresentation]

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

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

service_meta: ServiceMeta

warnings: list[Annotated[str]]

class cool_seq_tool.schemas.ToGenomicService(**data)

Service model response for cDNA -> genomic

g_data: Optional[GenomicRepresentation]

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

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

service_meta: ServiceMeta

warnings: list[Annotated[str]]

class cool_seq_tool.schemas.TranscriptExonData(**data)

Model containing transcript exon data.

chr: Annotated[str]

exon: Annotated[int]

exon_offset: Annotated[int]

gene: Annotated[str]

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

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

pos: Annotated[int]

strand: Strand

transcript: Annotated[str]

class cool_seq_tool.schemas.TranscriptExonDataResponse(**data)

Response model for Transcript Exon Data

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

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

service_meta: ServiceMeta

transcript_exon_data: Optional[TranscriptExonData]

warnings: list[Annotated[str]]

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'

class cool_seq_tool.schemas.TranscriptRequestBody(**data)

Define constraints for transcript exon to genomic coordinates request body

classmethod check_exon_start_and_exon_end(values)

Check that at least one of {exon_start, exon_end} is set

exon_end: Optional[Annotated[int]]

exon_end_offset: Optional[Annotated[int]]

exon_start: Optional[Annotated[int]]

exon_start_offset: Optional[Annotated[int]]

gene: Optional[Annotated[str]]

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

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

transcript: Annotated[str]