clj-hgvs

Clojure(Script) library for handling HGVS.

Features

clj-hgvs provides:

• Data structure for HGVS
• HGVS text parser
• HGVS text formatter

Installation

Clojure CLI/deps.edn:

clj-hgvs {:mvn/version "0.5.0"}

Leiningen/Boot:

[clj-hgvs "0.5.0"]

To use clj-hgvs with Clojure 1.8, you must include a dependency on clojure-future-spec.

Breaking Changes in 0.5.0

• Fix uncertain bases and amino acids format of ins and delins because HGVS nomenclature was updated.
  • DNA: ins(10) -> insN[10]
  • RNA: ins(10) -> insn[10]
  • Protein: ins10 -> insX[10]

Breaking Changes in 0.4.0

• HGVS data structure changes from map to record (clj-hgvs.core/HGVS).
• (n)cdna is renamed to (non-)coding-dna to avoid misunderstanding.

See CHANGELOG for more information.

Usage

Documentation

API Reference

Basics

(require '[clj-hgvs.core :as hgvs])

;; `parse` parses a HGVS text, returning a HGVS record.
(def hgvs1 (hgvs/parse "NM_005228.3:c.2573T>G"))

hgvs1
;;=> #clj_hgvs.core.HGVS
;;   {:transcript "NM_005228.3"
;;    :kind :coding-dna
;;    :mutation #clj_hgvs.mutation.DNASubstitution
;;              {:coord #clj_hgvs.coordinate.CodingDNACoordinate
;;                      {:position 2573
;;                       :offset 0
;;                       :region nil}
;;               :ref "T"
;;               :type ">"
;;               :alt "G"}}

;; `format` returns a HGVS text.
(hgvs/format hgvs1)
;;=> "NM_005228.3:c.2573T>G"

Tagged Literal

#clj-hgvs/hgvs tagged literal is useful for easy and readable definition of a HGVS data.

#clj-hgvs/hgvs "NM_005228.3:c.2573T>G"

Formatter Styles

clj-hgvs.core/format has various options for specifying HGVS styles.

(hgvs/format #clj-hgvs/hgvs "NM_005228.3:c.2307_2308insGCCAGCGTG"
             {:ins-format :count})
;;=> "NM_005228.3:c.2307_2308ins(9)"

(hgvs/format #clj-hgvs/hgvs "p.Leu858Arg"
             {:amino-acid-format :short})
;;=> "p.L858R"

See API reference for all formatter options.

Equivalence

clj-hgvs.core/== tests the fundamental equivalence of the given HGVS.

(hgvs/== #clj-hgvs/hgvs "NM_005228:c.2361G>A"
         #clj-hgvs/hgvs "NM_005228.4:c.2361G>A")
;;=> true

(hgvs/== #clj-hgvs/hgvs "p.K53Afs*9"
         #clj-hgvs/hgvs "p.Lys53Alafs")
;;=> true

(hgvs/== #clj-hgvs/hgvs "p.L858R"
         #clj-hgvs/hgvs "p.L858M")
;;=> false

Plain Map Representation

plain converts HGVS data to a plain map, and restore converts the map back to the HGVS data. These functions are useful for sending HGVS data through another codec.

(hgvs/plain #clj-hgvs/hgvs "NM_005228.3:c.2573T>G")
;;=> {:transcript "NM_005228.3"
;;    :kind "coding-dna"
;;    :mutation {:mutation "dna-substitution"
;;               :coord {:coordinate "coding-dna"
;;                       :position 2573
;;                       :offset 0
;;                       :region nil}
;;               :ref "T"
;;               :type ">"
;;               :alt "G"}}

(hgvs/restore *1)
;;=> #clj-hgvs/hgvs "NM_005228.3:c.2573T>G"

HGVS Repair

repair-hgvs-str attempts to repair an invalid HGVS text.

(hgvs/repair-hgvs-str "c.123_124GC>AA")
;;=> "c.123_124delGCinsAA"

The repair rules are based on frequent mistakes in popular public-domain databases such as dbSNP and ClinVar.

You may supply custom repair rules to the second argument:

(require '[clojure.string :as string]
         '[clj-hgvs.repairer :as repairer])

(defn lower-case-ext
  [s kind]
  (if (= kind :protein)
    (string/replace s #"EXT" "ext")
    s))

(def my-repairers (conj repairer/built-in-repairers
                        lower-case-ext))

(hgvs/repair-hgvs-str "p.*833EXT*?" my-repairers)
;;=> "p.*833ext*?"

License

Copyright 2017-2024 Xcoo, Inc.

Licensed under the Apache License, Version 2.0.