rtemis.a3

R implementation of the Amino Acid Annotation (A3) format — a structured JSON format for amino acid sequences with site, region, PTM, processing, and variant annotations.

Part of the rtemis-org/a3 monorepo, which provides A3 implementations in R, Python, Julia, TypeScript, and Rust.

Installation

R-universe

pak::repo_add(myuniverse = "https://rtemis-org.r-universe.dev")
pak::pak("rtemis.a3")

GitHub

pak::pak("rtemis-org/a3/r")

Quick Start

library(rtemis.a3)

a3 <- create_A3(
  sequence = "MKTAYIAKQR",
  site = list(
      "Active site" = annotation_position(c(3, 5),
    ),
  region = list(
    "Repeat 1" = annotation_range(rbind(c(1L, 4L)))
  ),
  ptm = list(
    Phosphorylation = annotation_position(c(7))
  ),
    uniprot_id  = "P12345",
    description = "Example protein",
    organism    = "Homo sapiens"
  )
)

Read / Write JSON

write_A3json(a3, "path/to/protein.json")
a3 <- read_A3json("path/to/protein.json")

API

Construction

Function	Description
`create_A3(sequence, site, region, ptm, ...)`	Create an A3 object
`annotation_position(x, type)`	Create a position-indexed annotation entry
`annotation_range(x, type)`	Create a range-indexed annotation entry
`annotation_variant(x, info)`	Create a variant annotation

I/O

Function	Description
`write_A3json(x, path)`	Write an A3 object to a JSON file
`read_A3json(path)`	Read an A3 object from a JSON file

S7 Class Hierarchy

A3
 ├── sequence:     A3Sequence
 ├── annotations:  A3Annotation
 │   ├── site:        named list of A3Site       (A3Position index)
 │   ├── region:      named list of A3Region     (A3Range index)
 │   ├── ptm:         named list of A3PTM        (A3Index — position or range)
 │   ├── processing:  named list of A3Processing (A3Index — position or range)
 │   └── variant:     list of A3Variant
 └── metadata:     A3Metadata
     ├── uniprot_id
     ├── description
     ├── reference
     └── organism