Site types

Target extraction assigns site: IDs from the genome assembly and the site’s 1-based inclusive genomic coordinates, including strand. A site that spans a splice junction lists its genomic segments in transcript order, separated by |. The same physical site keeps its ID across extraction order, target name versus gene ID, and overlapping target regions. Transcript offsets remain available in TranscriptSite.loci but do not define the shared site ID.

class ASOkai.Sites.Site(id, sequence, **kwargs)[source]

Bases: Serializable, ABC

Abstract base class for sites whose sequences are stored 5’ to 3’.

Parameters:

id (str)
sequence (Seq)

id: str

property sequence: Seq: Return the site sequence in the 5’ to 3’ direction.

class ASOkai.Sites.GenomicSite(chr, start, end, strand, sequence, id=None, genome=None, **kwargs)[source]

Bases: Site, GenomeElement

A sequence located at one genomic locus.

Parameters:

chr (str)
start (int)
end (int)
strand (Literal['+', '-'])
sequence (Seq)
id (str | None)
genome (Genome | None)

locus: Locus

File contract

This is the JSON record ASOkai stores for GenomicSite. 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__": "GenomicSite",
        "__module__": "ASOkai.Sites._genomic_site",
        "id": "example",
        "sequence": "A",
        "chr": "example",
        "start": 1,
        "end": 1,
        "strand": "+"
    },
    "objects": {}
}

Fields

JSON field	Details
`__class__`	Accepted value: `"GenomicSite"` Requirement: Required; keep unchanged in input files Meaning: Identifies this JSON object as GenomicSite. ASOkai writes it automatically.
`__module__`	Accepted value: `"ASOkai.Sites._genomic_site"` Requirement: Required; keep unchanged in input files Meaning: Tells ASOkai where GenomicSite is defined. ASOkai writes it automatically.
`id`	Accepted value: string Requirement: Required Meaning: Stable site identifier. Constructors derive it from the locus when omitted.
`chr`	Accepted value: string Requirement: Required Meaning: Chromosome containing the site.
`start`	Accepted value: integer Requirement: Required Meaning: The start position of the site (1-based inclusive).
`end`	Accepted value: integer Requirement: Required Meaning: The end position of the site (1-based inclusive).
`strand`	Accepted value: `"+"`, `"-"` Requirement: Required Meaning: Genomic strand containing the site.
`sequence`	Accepted value: string Requirement: Required Example: `"A"` Meaning: Site sequence in the 5'-to-3' direction.

class ASOkai.Sites.TranscriptSite(loci, sequence, id=None, **kwargs)[source]

Bases: Site

A sequence occurring at one or more transcript loci.

Parameters:

loci (list[TranscriptLocus])
sequence (Seq)
id (str | None)

loci: list[TranscriptLocus]

File contract

This is the JSON record ASOkai stores for TranscriptSite. 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.

Fields

JSON field	Details
`__class__`	Accepted value: `"TranscriptSite"` Requirement: Required; keep unchanged in input files Meaning: Identifies this JSON object as TranscriptSite. ASOkai writes it automatically.
`__module__`	Accepted value: `"ASOkai.Sites._transcript_site"` Requirement: Required; keep unchanged in input files Meaning: Tells ASOkai where TranscriptSite is defined. ASOkai writes it automatically.
`id`	Accepted value: string Requirement: Required Meaning: Stable site identifier. When omitted, it is derived from the first transcript locus.
`sequence`	Accepted value: string Requirement: Required Example: `"A"` Meaning: Site sequence in the 5'-to-3' direction.
`loci`	Accepted value: an array of objects Requirement: Required Meaning: Locations of this sequence on spliced transcripts.