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clj-hgvs

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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 "0.4.1"}

Leiningen/Boot:

[clj-hgvs "0.4.1"]

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

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.

License

Copyright 2017-2019 Xcoo, Inc.

Licensed under the Apache License, Version 2.0.

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