Target genes

class ASOkai.Targets.TargetGene(id, name, chr, start, end, strand, sequence, sites, genome=None, chromosome=None, **kwargs)

Bases: Serializable, Gene

A gene together with the target sites extracted from it.

Parameters:

• id (str)

• name (str)

• chr (str)

• start (int)

• end (int)

• strand (Literal['+', '-'])

• sequence (Seq)

• sites (Mapping[str, Site])

• genome (Genome | None)

• chromosome (Chromosome | None)

id: str

name: str

locus: Locus

property sequence: Seq

Return the target-gene sequence in the 5’ to 3’ direction.

property sites: list[Site]

Return the target sites in their creation order.

site_by_id(site_id)

Return the target site identified by site_id.

Parameters:

site_id (str)

Return type:

Site

add_site(site)

Add a target site whose ID is not already present.

Parameters:

site (Site)

Return type:

None

remove_site(site_id)

Remove the target site identified by site_id.

Parameters:

site_id (str)

Return type:

None

File contract

This is the JSON record ASOkai stores for TargetGene. A JSON file has a root value and an objects table. Objects used once are inline; repeatedly used objects move to the table and are linked by references. Nested records follow their own class contracts.

The __class__ and __module__ fields identify the object type. ASOkai adds them when writing JSON; keep the fixed values shown below when supplying an input file yourself.

Example file

{
    "root": {
        "__class__": "TargetGene",
        "__module__": "ASOkai.Targets._target_gene",
        "sequence": "A",
        "sites": {
            "example": {
                "__class__": "GenomicSite",
                "__module__": "ASOkai.Sites._genomic_site",
                "id": "example",
                "sequence": "A",
                "chr": "example",
                "start": 1,
                "end": 1,
                "strand": "+"
            }
        },
        "name": "example",
        "id": "example",
        "chr": "example",
        "start": 1,
        "end": 1,
        "strand": "+"
    },
    "objects": {}
}

Fields

JSON field	Details
__class__	Accepted value: "TargetGene" Requirement: Required; keep unchanged in input files Meaning: Identifies this JSON object as TargetGene. ASOkai writes it automatically.
__module__	Accepted value: "ASOkai.Targets._target_gene" Requirement: Required; keep unchanged in input files Meaning: Tells ASOkai where TargetGene is defined. ASOkai writes it automatically.
id	Accepted value: string Requirement: Required Meaning: Gene ID.
chr	Accepted value: string Requirement: Required Meaning: Chromosome containing the gene.
start	Accepted value: integer Requirement: Required Meaning: 1-based inclusive genomic start coordinate.
end	Accepted value: integer Requirement: Required Meaning: 1-based inclusive genomic end coordinate.
strand	Accepted value: "+", "-" Requirement: Required Meaning: Gene strand.
name	Accepted value: string Requirement: Required Meaning: Gene name.
sequence	Accepted value: string Requirement: Required Example: "A" Meaning: The gene sequence in the 5' to 3' direction.
sites	Accepted value: an object mapping string keys to GenomicSite objects or TranscriptSite objects Requirement: Required Meaning: Target sites keyed by their unique site IDs.