`biocantor.io.models`

Data models. These models allow for validation of inputs to a BioCantor model, acting as a JSON schema for serializing and deserializing the models.

Module Contents

Classes

`BaseModel`	Base for all of the models.
`ParentModel`	Data model that allows construction of a `Parent` object.
`FeatureIntervalModel`	Data model that allows construction of a `FeatureInterval` object.
`TranscriptIntervalModel`	Data model that allows construction of a `TranscriptInterval` object.
`VariantIntervalModel`	Data model that allows construction of `VariantInterval` object.
`GeneIntervalModel`	Data model that allows construction of `GeneInterval` object.
`FeatureIntervalCollectionModel`	Data model that allows construction of `FeatureCollection` object.
`VariantIntervalCollectionModel`	Data model that allows construction of `VariantCollection` object.
`AnnotationCollectionModel`	Data model that allows construction of `AnnotationCollection` object.

class biocantor.io.models.BaseModel

Base for all of the models.

class Meta

ordered = True

Schema :ClassVar[Type[marshmallow.Schema]]

class biocantor.io.models.ParentModel

Bases: BaseModel

Data model that allows construction of a Parent object.

seq :Optional[str]

alphabet :Optional[inscripta.biocantor.sequence.sequence.Alphabet]

sequence_name :Optional[str]

type :Optional[Union[inscripta.biocantor.sequence.sequence.SequenceType, str]]

start :Optional[int]

end :Optional[int]

strand :Optional[inscripta.biocantor.location.strand.Strand]

to_parent() → inscripta.biocantor.parent.Parent

class biocantor.io.models.FeatureIntervalModel

Bases: BaseModel

Data model that allows construction of a FeatureInterval object.

FeatureIntervals can have more than one type, and these types are arbitrary and not controlled by a biotype ontology.

interval_starts :List[int]

interval_ends :List[int]

strand :inscripta.biocantor.location.strand.Strand

qualifiers :Optional[Dict[str, List[Union[str, int, bool, float]]]]

sequence_name :Optional[str]

sequence_guid :Optional[uuid.UUID]

feature_interval_guid :Optional[uuid.UUID]

feature_guid :Optional[uuid.UUID]

feature_types :Optional[List[str]]

feature_name :Optional[str]

feature_id :Optional[str]

is_primary_feature :Optional[bool]

to_feature_interval(parent_or_seq_chunk_parent: Optional[inscripta.biocantor.parent.Parent] = None) → inscripta.biocantor.gene.feature.FeatureInterval

Construct a FeatureInterval from a FeatureIntervalModel.

A Parent can be provided to allow the sequence-retrieval functions to work.

static from_feature_interval(feature_interval: inscripta.biocantor.gene.feature.FeatureInterval) → FeatureIntervalModel: Convert a FeatureInterval to a FeatureIntervalModel

class biocantor.io.models.TranscriptIntervalModel

Bases: BaseModel

Data model that allows construction of a TranscriptInterval object.

exon_starts :List[int]

exon_ends :List[int]

strand :inscripta.biocantor.location.strand.Strand

cds_starts :Optional[List[int]]

cds_ends :Optional[List[int]]

cds_frames :Optional[List[inscripta.biocantor.gene.cds_frame.CDSFrame]]

qualifiers :Optional[Dict[str, List[Union[str, int, bool, float]]]]

is_primary_tx :Optional[bool]

transcript_id :Optional[str]

protein_id :Optional[str]

product :Optional[str]

transcript_symbol :Optional[str]

transcript_type :Optional[inscripta.biocantor.gene.biotype.Biotype]

sequence_name :Optional[str]

sequence_guid :Optional[uuid.UUID]

transcript_interval_guid :Optional[uuid.UUID]

transcript_guid :Optional[uuid.UUID]

to_transcript_interval(parent_or_seq_chunk_parent: Optional[inscripta.biocantor.parent.Parent] = None) → inscripta.biocantor.gene.transcript.TranscriptInterval

Construct a TranscriptInterval from a TranscriptIntervalModel.

A :class:`~biocantor.parent.Parent can be provided to allow the sequence-retrieval functions to work.

static from_transcript_interval(transcript_interval: inscripta.biocantor.gene.transcript.TranscriptInterval) → TranscriptIntervalModel: Convert to a TranscriptIntervalModel

class biocantor.io.models.VariantIntervalModel

Bases: BaseModel

Data model that allows construction of VariantInterval object.

start :int

end :int

sequence :str

variant_type :str

phase_block :Optional[int]

variant_interval_guid :Optional[uuid.UUID]

variant_guid :Optional[uuid.UUID]

variant_name :Optional[str]

variant_id :Optional[str]

qualifiers :Optional[Dict[str, List[Union[str, int, bool, float]]]]

static from_variant_interval(variant_interval: inscripta.biocantor.gene.variants.VariantInterval) → VariantIntervalModel: Convert to a VariantIntervalModel

to_variant_interval(parent_or_seq_chunk_parent: Optional[inscripta.biocantor.parent.Parent] = None) → inscripta.biocantor.gene.variants.VariantInterval

class biocantor.io.models.GeneIntervalModel

Bases: BaseModel

Data model that allows construction of GeneInterval object.

This is a container for one or more TranscriptInterval objects.

Has additional keys to help query the existing Gene table to see if this gene is there already.

transcripts :List[TranscriptIntervalModel]

gene_id :Optional[str]

gene_symbol :Optional[str]

gene_type :Optional[inscripta.biocantor.gene.biotype.Biotype]

locus_tag :Optional[str]

qualifiers :Optional[Dict[str, List[Union[str, int, bool, float]]]]

sequence_name :Optional[str]

sequence_guid :Optional[uuid.UUID]

gene_guid :Optional[uuid.UUID]

to_gene_interval(parent_or_seq_chunk_parent: Optional[inscripta.biocantor.parent.Parent] = None) → inscripta.biocantor.gene.GeneInterval

Produce a GeneInterval from a GeneIntervalModel.

This is the primary method of constructing a biocantor.gene.collections.GeneInterval.

static from_gene_interval(gene: inscripta.biocantor.gene.GeneInterval) → GeneIntervalModel

class biocantor.io.models.FeatureIntervalCollectionModel

Bases: BaseModel

Data model that allows construction of FeatureCollection object.

This is a container for one or more FeatureInterval objects.

Feature Collections do not have a type, but rather their type is the union of all of their child types.

feature_intervals :List[FeatureIntervalModel]

feature_collection_name :Optional[str]

feature_collection_id :Optional[str]

locus_tag :Optional[str]

feature_collection_type :Optional[str]

sequence_name :Optional[str]

sequence_guid :Optional[uuid.UUID]

feature_collection_guid :Optional[uuid.UUID]

qualifiers :Optional[Dict[str, List[Union[str, int, bool, float]]]]

to_feature_collection(parent_or_seq_chunk_parent: Optional[inscripta.biocantor.parent.Parent] = None) → inscripta.biocantor.gene.FeatureIntervalCollection: Produce a feature collection from a FeatureIntervalCollectionModel.

static from_feature_collection(feature_collection: inscripta.biocantor.gene.FeatureIntervalCollection) → FeatureIntervalCollectionModel

class biocantor.io.models.VariantIntervalCollectionModel

Bases: BaseModel

Data model that allows construction of VariantCollection object.

This is a container for one or more VariantInterval objects.

VariantIntervalCollection stores one or more variants on a phase block.

variant_intervals :List[VariantIntervalModel]

variant_collection_name :Optional[str]

variant_collection_id :Optional[str]

sequence_name :Optional[str]

sequence_guid :Optional[uuid.UUID]

variant_collection_guid :Optional[uuid.UUID]

qualifiers :Optional[Dict[str, List[Union[str, int, bool, float]]]]

static from_variant_interval_collection(variant_collection: inscripta.biocantor.gene.variants.VariantIntervalCollection) → VariantIntervalCollectionModel: Convert to a VariantIntervalModel

to_variant_interval_collection(parent_or_seq_chunk_parent: Optional[inscripta.biocantor.parent.Parent] = None) → inscripta.biocantor.gene.variants.VariantIntervalCollection: Produce a variant collection from a VariantIntervalCollectionModel.

class biocantor.io.models.AnnotationCollectionModel

Bases: BaseModel

Data model that allows construction of AnnotationCollection object.

This is the highest level type of container, and is most often used to store everything for a genomic interval query.

This container has optional start and end members because it can be the product of genomic interval queries that are larger than the contents of the object. If those values are not set, when an :class:~biocantor.gene.collections.AnnotationCollection` is instantiated, they will be inferred.

Additionally, this container has an optional completely_within member that determines if a range query that produced this container was done using the completely_within flag. If this is True, then it may be the case that start is larger than the smallest start position of a member of this collection, and vice versa for end.

feature_collections :List[FeatureIntervalCollectionModel]

genes :List[GeneIntervalModel]

variant_collections :List[VariantIntervalCollectionModel]

name :Optional[str]

id :Optional[str]

sequence_name :Optional[str]

sequence_guid :Optional[uuid.UUID]

sequence_path :Optional[str]

qualifiers :Optional[Dict[str, List[Union[str, int, bool, float]]]]

start :Optional[int]

end :Optional[int]

completely_within :Optional[bool]

parent_or_seq_chunk_parent :Optional[ParentModel]

post_dump(data, model, many=False): If the object being dumped is an AnnotationCollection, convert the _parent_or_seq_chunk_parent value to parent_or_seq_chunk_parent.

to_annotation_collection(parent_or_seq_chunk_parent: Optional[inscripta.biocantor.parent.Parent] = None) → inscripta.biocantor.gene.collections.AnnotationCollection: Produce an AnnotationCollection from this model.

static from_annotation_collection(annotation_collection: inscripta.biocantor.gene.collections.AnnotationCollection, chromosome_relative_coordinates: bool = True, export_parent: bool = False) → AnnotationCollectionModel: Convert back to AnnotationCollectionModel.

biocantor.io.models

Module Contents

Classes

`biocantor.io.models`