hgvsparser: buildHGVS.R annotate

annotate buildHGVS.R @ 0:c12a4d187121 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0

author	iuc
date	Fri, 07 Jun 2024 15:21:07 +0000
parents
children

rev	line source
0 c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	1 # Copyright (C) 2018 Jochen Weile, Roth Lab
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	2 #
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	3 # This file is part of hgvsParseR.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	4 #
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	5 # hgvsParseR is free software: you can redistribute it and/or modify
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	6 # it under the terms of the GNU General Public License as published by
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	7 # the Free Software Foundation, either version 3 of the License, or
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	8 # (at your option) any later version.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	9 #
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	10 # hgvsParseR is distributed in the hope that it will be useful,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	13 # GNU General Public License for more details.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	14 #
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	15 # You should have received a copy of the GNU General Public License
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	16 # along with hgvsParseR. If not, see <https://www.gnu.org/licenses/>.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	17
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	18 #' Genomic HGVS Builder
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	19 #'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	20 #' A constructor for a genomic-level HGVS builder object. The object contains a collection of functions
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	21 #' for building genomic HGVS strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	22 #'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	23 #' The resulting object encapsulates the following functions:
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	24 #' \itemize{
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	25 #' \item{substitution(pos,ancestral,variant)} Genomic substitution variants.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	26 #' pos = position (integer); ancestral = ancestral nucleotide [ACGT];
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	27 #' variant = variant nucleotide [ACGT]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	28 #' \item{deletion(start,stop)} Genomic deletion. start = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	29 #' stop = stop position (integer)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	30 #' \item{inversion(start,stop)} Genomic inversion. start = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	31 #' stop = stop position (integer)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	32 #' \item{duplication(start,stop)} Genomic duplication. start = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	33 #' stop = stop position (integer)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	34 #' \item{insertion(start,variant)} Genomic insertion. start = position immediately preceeding
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	35 #' the insertion (integer); seq = inserted nucleotide sequence [ACGT]+
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	36 #' \item{delins(start,stop,variant)} Genomic deletion and insertion. start = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	37 #' stop = stop position relative to the reference (integer); seq = inserted nucleotide sequence [ACGT]+
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	38 #' \item{cis(...)} Multi-variant phased in cis. Parameters are genomic HGVS strings for the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	39 #' corresponding single mutants
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	40 #' \item{trans(...)} Multi-variant phased in trans. Parameters are genomic HGVS strings for the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	41 #' corresponding single mutants
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	42 #' \item{nophase(...)} Multi-variant with unknown phasing. Parameters are genomic HGVS strings for the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	43 #' corresponding single mutants
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	44 #' }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	45 #'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	46 #' @return A \code{hgvs.builder.g} object with functions for building genomic HGVS strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	47 #' The individual functions return single-element character vectors containing these strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	48 #' @keywords HGVS builder
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	49 #' @export
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	50 #' @examples
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	51 #' builder <- new.hgvs.builder.g()
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	52 #' string1 <- builder$substitution(123,"A","G")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	53 #' string2 <- builder$delins(123,129,"ATTG")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	54 #' string3 <- with(builder,cis(substitution(123,"A","C"),substitution(231,"G","A")))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	55
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	56 new.hgvs.builder.g <- function() {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	57
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	58 substitution <- function(pos,ancestral,variant) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	59 if (!is.numeric(pos) \|\| pos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	60 if (!is.character(ancestral) \|\| !(ancestral %in% c("A","C","G","T"))) stop("ancestral must be single nucleotide")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	61 if (!is.character(variant) \|\| !(variant %in% c("A","C","G","T"))) stop("variant must be single nucleotide")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	62 paste0("g.",pos,ancestral,">",variant)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	63 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	64
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	65 deletion <- function(start,stop) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	66 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	67 if (!is.numeric(stop)) stop("stop must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	68 if (start > stop) stop("start must be upstream of stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	69 paste0("g.",start,"_",stop,"del")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	70 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	71
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	72 inversion <- function(start,stop) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	73 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	74 if (!is.numeric(stop)) stop("stop must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	75 if (start > stop) stop("start must be upstream of stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	76 paste0("g.",start,"_",stop,"inv")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	77 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	78
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	79 duplication <- function(start,stop) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	80 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	81 if (!is.numeric(stop)) stop("stop must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	82 if (start > stop) stop("start must be upstream of stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	83 paste0("g.",start,"_",stop,"dup")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	84 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	85
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	86 insertion <- function(start,seq) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	87 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	88 if (!is.character(seq) \|\| regexpr("^[ACGT]+$",seq) < 1) stop("variant must be nucleotide sequence")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	89 paste0("g.",start,"_",start+1,"ins",seq)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	90 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	91
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	92 delins <- function(start,stop,seq) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	93 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	94 if (!is.numeric(stop)) stop("stop must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	95 if (start > stop) stop("start must be upstream of stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	96 if (!is.character(seq) \|\| regexpr("^[ACGT]+$",seq) < 1) stop("variant must be nucleotide sequence")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	97 paste0("g.",start,"_",stop,"delins",seq)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	98 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	99
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	100 cis <- function(...) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	101 strings <- list(...)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	102 if (!all(sapply(strings,is.character))) stop("all arguments must be HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	103 strings <- unlist(strings)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	104 if (!all(substr(strings,1,2)=="g.")) stop("all arguments must be genomic HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	105 bodies <- substr(strings,3,nchar(strings))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	106 paste0("g.[",paste(bodies,collapse=";"),"]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	107 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	108
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	109 trans <- function(...) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	110 strings <- list(...)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	111 if (!all(sapply(strings,is.character))) stop("all arguments must be HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	112 strings <- unlist(strings)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	113 if (!all(substr(strings,1,2)=="g.")) stop("all arguments must be genomic HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	114 bodies <- substr(strings,3,nchar(strings))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	115 paste0("g.[",paste(bodies,collapse="];["),"]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	116 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	117
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	118 nophase <- function(...) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	119 strings <- list(...)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	120 if (!all(sapply(strings,is.character))) stop("all arguments must be HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	121 strings <- unlist(strings)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	122 if (!all(substr(strings,1,2)=="g.")) stop("all arguments must be genomic HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	123 bodies <- substr(strings,3,nchar(strings))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	124 paste0("g.[",paste(bodies,collapse="(;)"),"]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	125 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	126
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	127 return(structure(list(
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	128 substitution=substitution,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	129 deletion=deletion,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	130 inversion=inversion,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	131 duplication=duplication,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	132 insertion=insertion,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	133 delins=delins,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	134 cis=cis,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	135 trans=trans,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	136 nophase=nophase
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	137 ),class="hgvs.builder.g"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	138 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	139
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	140 print.hgvs.builder.g <- function() {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	141 cat("Genomic HGVS string builder. Use $ operator to access functions.")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	142 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	143
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	144
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	145
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	146 #' Coding Sequence HGVS Builder
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	147 #'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	148 #' A constructor for a CDS (=coding sequence) HGVS builder object. The object contains a collection of functions
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	149 #' for building CDS HGVS strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	150 #' The resulting object encapsulates the following functions:
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	151 #' \itemize{
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	152 #' \item{substitution(pos,ancestral,variant,posOffset=0)} CDS substitution variants.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	153 #' pos = position (integer); ancestral = ancestral nucleotide [ACGT];
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	154 #' variant = variant nucleotide [ACGT]; posOffset = offset from the position when
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	155 #' crossing exon-intron borders (integer, defaults to 0)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	156 #' \item{deletion(start,stop,startOffset=0,stopOffset=0)} CDS deletion. start = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	157 #' stop = stop position (integer); startOffset = offset from the start position when
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	158 #' crossing exon-intron borders (integer, defaults to 0); stopOffset = offset from the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	159 #' stop position when crossing exon-intron borders (integer, defaults to 0)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	160 #' \item{inversion(start,stop,startOffset=0,stopOffset=0)} CDS inversion. start = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	161 #' stop = stop position (integer); startOffset = offset from the start position when
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	162 #' crossing exon-intron borders (integer, defaults to 0); stopOffset = offset from the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	163 #' stop position when crossing exon-intron borders (integer, defaults to 0)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	164 #' \item{duplication(start,stop,startOffset=0,stopOffset=0)} CDS duplication. start = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	165 #' stop = stop position (integer); startOffset = offset from the start position when
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	166 #' crossing exon-intron borders (integer, defaults to 0); stopOffset = offset from the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	167 #' stop position when crossing exon-intron borders (integer, defaults to 0)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	168 #' \item{insertion(start,variant,startOffset=0)} CDS insertion. start = position immediately preceeding
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	169 #' the insertion (integer); seq = inserted nucleotide sequence [ACGT]+ ;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	170 #' startOffset = offset from the start position when crossing exon-intron borders
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	171 #' (integer, defaults to 0)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	172 #' \item{delins(start,stop,variant,startOffset=0,stopOffset=0)} CDS deletion and insertion. start = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	173 #' stop = stop position relative to the reference (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	174 #' seq = inserted nucleotide sequence [ACGT]+ ; startOffset = offset from the start position when
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	175 #' crossing exon-intron borders (integer, defaults to 0); stopOffset = offset from the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	176 #' stop position when crossing exon-intron borders (integer, defaults to 0)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	177 #' \item{cis(...)} Multi-variant phased in cis. Parameters are coding HGVS strings for the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	178 #' corresponding single mutants
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	179 #' \item{trans(...)} Multi-variant phased in trans. Parameters are coding HGVS strings for the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	180 #' corresponding single mutants
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	181 #' \item{nophase(...)} Multi-variant with unknown phasing. Parameters are coding HGVS strings for the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	182 #' corresponding single mutants
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	183 #' }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	184 #'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	185 #' @return A \code{hgvs.builder.c} object with functions for building coding HGVS strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	186 #' The individual functions return single-element character vectors containing these strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	187 #' @keywords HGVS builder
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	188 #' @export
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	189 #' @examples
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	190 #' builder <- new.hgvs.builder.c()
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	191 #' string1 <- builder$substitution(123,"A","G",posOffset=2)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	192 #' string2 <- builder$delins(123,129,"ATTG")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	193 #' string3 <- with(builder,cis(substitution(123,"A","C"),substitution(231,"G","A")))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	194
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	195 new.hgvs.builder.c <- function() {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	196
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	197 offsetStr <- function(offset) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	198 if (offset==0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	199 ""
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	200 } else if (offset > 0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	201 paste0("+",offset)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	202 } else if (offset < 0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	203 as.character(offset)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	204 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	205 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	206
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	207 substitution <- function(pos,ancestral,variant,posOffset=0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	208 if (!is.numeric(pos) \|\| pos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	209 if (!is.numeric(posOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	210 if (!is.character(ancestral) \|\| !(ancestral %in% c("A","C","G","T"))) stop("ancestral must be single nucleotide")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	211 if (!is.character(variant) \|\| !(variant %in% c("A","C","G","T"))) stop("variant must be single nucleotide")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	212 paste0("c.",pos,offsetStr(posOffset),ancestral,">",variant)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	213 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	214
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	215 deletion <- function(start,stop,startOffset=0,stopOffset=0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	216 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	217 if (!is.numeric(stop)) stop("stop must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	218 if (!is.numeric(startOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	219 if (!is.numeric(stopOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	220 if (start+startOffset > stop+stopOffset) stop("start must be before stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	221 paste0("c.",start,offsetStr(startOffset),"_",stop,offsetStr(stopOffset),"del")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	222 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	223
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	224 inversion <- function(start,stop,startOffset=0,stopOffset=0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	225 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	226 if (!is.numeric(stop)) stop("stop must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	227 if (!is.numeric(startOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	228 if (!is.numeric(stopOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	229 if (start+startOffset >= stop+stopOffset) stop("start must be before stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	230 paste0("c.",start,offsetStr(startOffset),"_",stop,offsetStr(stopOffset),"inv")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	231 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	232
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	233 duplication <- function(start,stop,startOffset=0,stopOffset=0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	234 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	235 if (!is.numeric(stop)) stop("stop must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	236 if (!is.numeric(startOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	237 if (!is.numeric(stopOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	238 if (start+startOffset > stop+stopOffset) stop("start must be before stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	239 paste0("c.",start,offsetStr(startOffset),"_",stop,offsetStr(stopOffset),"dup")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	240 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	241
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	242 insertion <- function(start,seq,startOffset=0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	243 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	244 if (!is.character(seq) \|\| regexpr("^[ACGT]+$",seq) < 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	245 stop("variant must be nucleotide sequence")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	246 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	247 if (!is.numeric(startOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	248 stop <- if (startOffset != 0) start else start+1
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	249 stopOffset <- if (startOffset != 0) startOffset+1 else startOffset
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	250 paste0("c.",start,offsetStr(startOffset),"_",stop,offsetStr(stopOffset),"ins",seq)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	251 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	252
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	253 delins <- function(start,stop,seq,startOffset=0,stopOffset=0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	254 if (!is.numeric(start)) stop("start must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	255 if (!is.numeric(stop)) stop("stop must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	256 if (!is.numeric(startOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	257 if (!is.numeric(stopOffset)) stop("offset must be an integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	258 if (start+startOffset > stop+stopOffset) stop("start must be before stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	259 if (!is.character(seq) \|\| regexpr("^[ACGT]+$",seq) < 1) stop("variant must be nucleotide sequence")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	260 paste0("c.",start,offsetStr(startOffset),"_",stop,offsetStr(stopOffset),"delins",seq)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	261 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	262
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	263 cis <- function(...) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	264 strings <- list(...)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	265 if (!all(sapply(strings,is.character))) stop("all arguments must be HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	266 strings <- unlist(strings)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	267 if (!all(substr(strings,1,2)=="c.")) stop("all arguments must be coding HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	268 bodies <- substr(strings,3,nchar(strings))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	269 paste0("c.[",paste(bodies,collapse=";"),"]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	270 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	271
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	272 trans <- function(...) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	273 strings <- list(...)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	274 if (!all(sapply(strings,is.character))) stop("all arguments must be HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	275 strings <- unlist(strings)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	276 if (!all(substr(strings,1,2)=="c.")) stop("all arguments must be coding HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	277 bodies <- substr(strings,3,nchar(strings))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	278 paste0("c.[",paste(bodies,collapse="];["),"]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	279 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	280
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	281 nophase <- function(...) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	282 strings <- list(...)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	283 if (!all(sapply(strings,is.character))) stop("all arguments must be HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	284 strings <- unlist(strings)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	285 if (!all(substr(strings,1,2)=="c.")) stop("all arguments must be coding HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	286 bodies <- substr(strings,3,nchar(strings))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	287 paste0("c.[",paste(bodies,collapse="(;)"),"]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	288 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	289
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	290 return(structure(list(
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	291 substitution=substitution,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	292 deletion=deletion,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	293 inversion=inversion,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	294 duplication=duplication,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	295 insertion=insertion,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	296 delins=delins,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	297 cis=cis,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	298 trans=trans,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	299 nophase=nophase
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	300 ),class="hgvs.builder.c"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	301 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	302
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	303 print.hgvs.builder.c <- function() {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	304 cat("Coding-sequence HGVS string builder. Use $ operator to access functions.")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	305 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	306
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	307
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	308
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	309 #' Protein HGVS Builder
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	310 #'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	311 #' A constructor for a protein-level HGVS builder object. The object contains a collection of functions
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	312 #' for building protein HGVS strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	313 #'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	314 #' The resulting object encapsulates the following functions:
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	315 #' \itemize{
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	316 #' \item{synonymous()} A synonymous variant. No parameters required.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	317 #' \item{synonymous(pos,ancestral)} Unofficial (yet frequently used) version of synonymous variant syntax.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	318 #' pos = position (integer); ancestral = ancestral amino acid in one-letter or three-letter code.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	319 #' \item{substitution(pos,ancestral,variant)} AA substitution variants.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	320 #' pos = position (integer); ancestral = ancestral amino acid in one-letter or three-letter code;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	321 #' variant = variant amino acid in one-letter or three-letter code
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	322 #' \item{deletion(startPos,startAA,endPos,endAA)} AA deletion. startPos = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	323 #' startAA = start amino acid in one-letter or three-letter code;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	324 #' endPos = stop position (integer); endAA = start amino acid in one-letter or three-letter code
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	325 #' \item{duplication(startPos,startAA,endPos,endAA)} AA duplication. startPos = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	326 #' startAA = start amino acid in one-letter or three-letter code;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	327 #' endPos = stop position (integer); endAA = start amino acid in one-letter or three-letter code
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	328 #' \item{insertion(leftPos,leftAA,rightAA,seq)} AA insertion. leftPos = position immediately preceeding
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	329 #' the insertion (integer); leftAA = corresponding amino acid in one-letter or three-letter code;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	330 #' rightAA = amino acid to the right of the insertion, in one-letter or three-letter code;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	331 #' seq = inserted amino acid sequence, given as a character vector containing the individual
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	332 #' one-letter or three-letter amino acid codes.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	333 #' \item{delins(startPos,startAA,endPos,endAA,seq)} AA deletion and insertion.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	334 #' startPos = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	335 #' startAA = start amino acid in one-letter or three-letter code;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	336 #' endPos = stop position (integer); endAA = start amino acid in one-letter or three-letter code;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	337 #' seq = inserted amino acid sequence, given as a character vector containing the individual
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	338 #' one-letter or three-letter amino acid codes.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	339 #' \item{frameshift(startPos,startAA,variantAA=NA,newStop=NA)} Frameshift variant.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	340 #' startPos = start position (integer);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	341 #' startAA = start amino acid in one-letter or three-letter code;
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	342 #' variantAA = amino acid replacing the start position in the frameshift sequence,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	343 #' given in one-letter or three-letter code, or \code{NA} to omit (default);
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	344 #' newStop = the position of the nearest coding resulting from the frameshift,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	345 #' or \code{NA} to omit (default).
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	346 #' \item{cis(...)} Multi-variant phased in cis. Parameters are coding HGVS strings for the
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	347 #' corresponding single mutants. As phasing in trans would be nonsensical in a protein context,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	348 #' the \code{trans()} and \code{nophase()} methods are not provided here.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	349 #' }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	350 #'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	351 #' @return A \code{hgvs.builder.g} object with functions for building genomic HGVS strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	352 #' The individual functions return single-element character vectors containing these strings.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	353 #' @keywords HGVS builder
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	354 #' @export
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	355 #' @examples
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	356 #' builder <- new.hgvs.builder.g()
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	357 #' string1 <- builder$substitution(123,"R","K")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	358 #' string2 <- builder$delins(123,"Arg",152,"Leu",c("Lys","Trp","Ser"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	359 #' string3 <- with(builder,cis(substitution(123,"R","K"),deletion(125,"S",152,"L")))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	360
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	361
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	362 new.hgvs.builder.p <- function(aacode=c(1,3)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	363
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	364 aacode <- aacode[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	365 if (!is.numeric(aacode) && !(aacode %in% c(1,3))) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	366 stop("Invalid aacode parameter, only 1 or 3 allowed!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	367 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	368
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	369 one2three <- c(A="Ala",C="Cys",D="Asp",E="Glu",F="Phe",G="Gly",H="His",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	370 I="Ile",K="Lys",L="Leu",M="Met",N="Asn",P="Pro",Q="Gln",R="Arg",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	371 S="Ser",T="Thr",V="Val",W="Trp",Y="Tyr",`*`="Ter")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	372 three2one <- c(Ala="A",Arg="R",Asn="N",Asp="D",Cys="C",Gln="Q",Glu="E",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	373 Gly="G",His="H",Ile="I",Leu="L",Lys="K",Met="M",Phe="F",Pro="P",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	374 Ser="S",Thr="T",Trp="W",Tyr="Y",Val="V",Ter="*")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	375
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	376 enforceCode <- function(aa) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	377 if (aa %in% one2three) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	378 if (aacode == 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	379 three2one[[aa]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	380 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	381 aa
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	382 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	383 } else if (aa %in% three2one) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	384 if (aacode == 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	385 aa
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	386 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	387 one2three[[aa]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	388 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	389 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	390 stop("Invalid AA code")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	391 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	392 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	393
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	394 synonymous <- function(pos=NULL,ancestral=NULL) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	395 if (is.null(pos) \|\| is.null(ancestral)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	396 return("p.=")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	397 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	398 if (!is.numeric(pos) \|\| pos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	399 if (!is.character(ancestral) \|\| !(ancestral %in% c(one2three,three2one))) stop("ancestral must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	400 ancestral <- enforceCode(ancestral)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	401 paste0("p.",ancestral,pos,"=")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	402 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	403
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	404 substitution <- function(pos,ancestral,variant) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	405 if (!is.numeric(pos) \|\| pos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	406 if (!is.character(ancestral) \|\| !(ancestral %in% c(one2three,three2one))) stop("ancestral must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	407 if (!is.character(variant) \|\| !(variant %in% c(one2three,three2one))) stop("variant must be single amino acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	408 ancestral <- enforceCode(ancestral)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	409 variant <- enforceCode(variant)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	410 paste0("p.",ancestral,pos,variant)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	411 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	412
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	413 deletion <- function(startPos,startAA,endPos,endAA) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	414 if (!is.numeric(startPos) \|\| startPos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	415 if (!is.numeric(endPos) \|\| endPos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	416 if (startPos > endPos) stop("start must be upstream of stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	417 if (!is.character(startAA) \|\| !(startAA %in% c(one2three,three2one))) stop("startAA must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	418 if (!is.character(endAA) \|\| !(endAA %in% c(one2three,three2one))) stop("endAA must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	419 startAA <- enforceCode(startAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	420 endAA <- enforceCode(endAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	421 if (startPos==endPos) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	422 paste0("p.",startAA,startPos,"del")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	423 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	424 paste0("p.",startAA,startPos,"_",endAA,endPos,"del")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	425 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	426 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	427
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	428 duplication <- function(startPos,startAA,endPos,endAA) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	429 if (!is.numeric(startPos) \|\| startPos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	430 if (!is.numeric(endPos) \|\| endPos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	431 if (startPos >= endPos) stop("start must be upstream of stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	432 if (!is.character(startAA) \|\| !(startAA %in% c(one2three,three2one)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	433 stop("startAA must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	434 if (!is.character(endAA) \|\| !(endAA %in% c(one2three,three2one)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	435 stop("endAA must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	436 startAA <- enforceCode(startAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	437 endAA <- enforceCode(endAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	438 paste0("p.",startAA,startPos,"_",endAA,endPos,"dup")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	439 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	440
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	441 insertion <- function(leftPos,leftAA,rightAA,seq) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	442 if (!is.numeric(leftPos) \|\| leftPos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	443 if (!is.character(leftAA) \|\| !(leftAA %in% c(one2three,three2one)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	444 stop("leftAA must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	445 if (!is.character(rightAA) \|\| !(rightAA %in% c(one2three,three2one)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	446 stop("rightAA must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	447 if (!is.character(seq) \|\| !all(sapply(seq,function(x) x %in% c(one2three,three2one))))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	448 stop("seq must be a vector of amino acids")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	449 rightPos <- leftPos+1
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	450 leftAA <- enforceCode(leftAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	451 rightAA <- enforceCode(rightAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	452 seq <- paste(sapply(seq,enforceCode),collapse="")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	453 paste0("p.",leftAA,leftPos,"_",rightAA,rightPos,"ins",seq)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	454 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	455
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	456 delins <- function(startPos,startAA,endPos,endAA,seq) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	457 if (!is.numeric(startPos) \|\| startPos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	458 if (!is.numeric(endPos) \|\| endPos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	459 if (startPos > endPos) stop("start must be upstream of stop")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	460 if (!is.character(startAA) \|\| !(startAA %in% c(one2three,three2one)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	461 stop("startAA must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	462 if (!is.character(endAA) \|\| !(endAA %in% c(one2three,three2one)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	463 stop("endAA must be single amimo acid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	464 if (!is.character(seq) \|\| !all(sapply(seq,function(x) x %in% c(one2three,three2one))))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	465 stop("seq must be a vector of amino acids")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	466 startAA <- enforceCode(startAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	467 endAA <- enforceCode(endAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	468 seq <- paste(sapply(seq,enforceCode),collapse="")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	469 paste0("p.",startAA,startPos,"_",endAA,endPos,"delins",seq)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	470 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	471
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	472 frameshift <- function(startPos,startAA,variantAA=NA,newStop=NA) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	473 if (!is.numeric(startPos) \|\| startPos < 1) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	474 if (!is.na(newStop) && (!is.numeric(newStop) \|\| newStop < 1)) stop("position must be a positive integer")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	475 if (!is.character(startAA) \|\| !(startAA %in% c(one2three,three2one)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	476 stop("startAA must be single amimo acid or NA")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	477 if (!is.na(variantAA) && (!is.character(startAA) \|\| !(startAA %in% c(one2three,three2one))))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	478 stop("variantAA must be single amimo acid or NA")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	479 startAA <- enforceCode(startAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	480 if (is.na(variantAA)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	481 variantAA <- ""
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	482 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	483 variantAA <- enforceCode(variantAA)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	484 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	485 if (is.na(newStop)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	486 newStop <- ""
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	487 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	488 newStop <- paste0("*",newStop)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	489 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	490 paste0("p.",startAA,startPos,variantAA,"fs",newStop)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	491 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	492
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	493 cis <- function(...) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	494 strings <- list(...)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	495 if (!all(sapply(strings,is.character))) stop("all arguments must be HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	496 strings <- unlist(strings)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	497 if (!all(substr(strings,1,2)=="p.")) stop("all arguments must be protein HGVS strings")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	498 bodies <- substr(strings,3,nchar(strings))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	499 paste0("p.[",paste(bodies,collapse=";"),"]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	500 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	501
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	502 return(structure(list(
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	503 synonymous=synonymous,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	504 substitution=substitution,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	505 deletion=deletion,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	506 duplication=duplication,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	507 insertion=insertion,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	508 delins=delins,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	509 frameshift=frameshift,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	510 cis=cis
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	511 ),class="hgvs.builder.p"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	512 }

Mercurial > repos > iuc > hgvsparser

annotate buildHGVS.R @ 0:c12a4d187121 draft default tip