clj-hgvs.core — clj-hgvs 0.3.0

Functions to handle HGVS. See http://varnomen.hgvs.org/ for the detail HGVS nomenclature.

format clj/s

(format hgvs)

(format hgvs opts)

Returns a HGVS string representing the given HGVS map. The second argument is an optional map to specify style: :show-bases? - displays additional bases, e.g. g.6_8delTGC, default false. :ins-format - bases style of insertion, default :auto. <:auto|:bases|:count> :range-format - range style, default :auto. <:auto|:bases|:coord> :amino-acid-format - amino acid style of protein HGVS, default :long. <:long|:short> :show-ter-site? - displays a new ter codon site of protein frame shift, default false. :ter-format - ter codon style of protein frame shift and extension, default :long. <:long|:short>

hgvs clj/s

(hgvs transcript kind mutation)

Constructor of HGVS map. Throws an exception if any input is illegal.

normalize clj/s

(normalize s)

Reformats the HGVS string s, returning the normalized HGVS string. Default values are used for style options. Throws an exception when an illegal HGVS string is supplied.

parse clj/s

(parse s)

Parses a HGVS string s, returning a map representing the HGVS.

plain clj/s

(plain hgvs)

Returns a plain map representing the given HGVS. This function is useful for sending data through another codec. Use restore to retrieve original HGVS data.

restore clj/s

(restore m)

Restores a plain map to a suitable HGVS data structure. This function is useful for sending data through another codec.