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https://github.com/chrovis/clj-hgvs
Clojure(Script) library for handling HGVS
https://github.com/chrovis/clj-hgvs
bioinformatics clojure clojurescript hgvs
Last synced: 3 months ago
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Clojure(Script) library for handling HGVS
- Host: GitHub
- URL: https://github.com/chrovis/clj-hgvs
- Owner: chrovis
- License: apache-2.0
- Created: 2017-03-28T10:40:43.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-10-16T05:55:19.000Z (4 months ago)
- Last Synced: 2024-10-18T15:13:30.708Z (4 months ago)
- Topics: bioinformatics, clojure, clojurescript, hgvs
- Language: Clojure
- Size: 399 KB
- Stars: 7
- Watchers: 11
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# clj-hgvs
[](https://clojars.org/clj-hgvs)
[](https://github.com/chrovis/clj-hgvs/actions/workflows/build.yml)
[](https://codecov.io/gh/chrovis/clj-hgvs)
Clojure(Script) library for handling [HGVS](https://hgvs-nomenclature.org/).
## Features
clj-hgvs provides:
* Data structure for HGVS
* HGVS text parser
* HGVS text formatter
## Installation
Clojure CLI/deps.edn:
```clojure
clj-hgvs {:mvn/version "0.5.0"}
```
Leiningen/Boot:
```clojure
[clj-hgvs "0.5.0"]
```
To use clj-hgvs with Clojure 1.8, you must include a dependency on
[clojure-future-spec](https://github.com/tonsky/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](CHANGELOG.md) for more information.
## Usage
### Documentation
[API Reference](https://chrovis.github.io/clj-hgvs/)
### Basics
```clojure
(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.
```clojure
#clj-hgvs/hgvs "NM_005228.3:c.2573T>G"
```
### Formatter Styles
`clj-hgvs.core/format` has various options for specifying HGVS styles.
```clojure
(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](https://chrovis.github.io/clj-hgvs/clj-hgvs.core.html#var-format)
for all formatter options.
### Equivalence
`clj-hgvs.core/==` tests the fundamental equivalence of the given HGVS.
```clojure
(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.
```clojure
(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.
```clojure
(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:
```clojure
(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.](https://xcoo.jp/)
Licensed under the [Apache License, Version 2.0](LICENSE).