clj-hgvs.core — clj-hgvs 0.2.0

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> :ter-format - ter codon style of protein frame shift. <:long|:short>

hgvs clj/s

(hgvs transcript kind mutation)

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

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.