hgvsparser: parseHGVS.R annotate

annotate parseHGVS.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 #' HGVS Parser
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 #' Parses HGVS strings
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	21 #' @param strings A character vector containing the HGVS strings
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	22 #' @param aacode allowed values: 1, 3, or NA. Determines whether 1-letter codes or 3-letter codes should be forced. NA uses input format.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	23 #' @return A \code{data.frame} with the following columns:
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	24 #' @keywords HGVS parsing
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	25 #' @export
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	26 #' @examples
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	27 #' result <- parseHGVS(c("g.1318G>T","c.123_125inv","p.R123_L152del"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	28
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	29 parseHGVS <- function(strings,aacode=c(NA,1,3)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	30
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	31 #Check that parameters are valid
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	32 if (!is.character(strings)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	33 stop("Input for 'parse' function must be a character vector! Found '",class(strings),"' instead.")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	34 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	35
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	36 aacode <- aacode[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	37 if (!is.na(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	38 warning("Invalid aacode parameter, defaulting to NA!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	39 aacode <- NA
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	40 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	41
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	42 #Helper function: turns a list of lists (lol) in to a dataframe
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	43 to.df <- function(lol) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	44 colnames <- unique(do.call(c,lapply(lol,names)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	45 columns <- lapply(colnames,function(cn) sapply(lol,function(row) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	46 if (cn %in% names(row)) row[[cn]] else NA
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	47 }))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	48 names(columns) <- colnames
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	49 empty <- which(sapply(columns,function(xs)all(is.na(xs))))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	50 columns[empty] <- NULL
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	51 do.call(data.frame,columns)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	52 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	53
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	54 # ###
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	55 # # Binds matrices of same size together to a 3D matrix, analogously
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	56 # # to cbind and rbind.
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 # zbind <- function(...) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	59 # x <- list(...)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	60 # y <- array(0,dim=c(nrow(x[[1]]),ncol(x[[1]]),length(x)),dimnames=dimnames(x[[1]]))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	61 # for (i in 1:length(x)) y[,,i] <- x[[i]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	62 # y
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
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	66 ###
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	67 # Function to locally excise regex groups from string vectors.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	68 # I.e. only extract the first occurrence of each group within each string.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	69 # x = string vector
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	70 # re = regular expression with groups
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 extract.groups <- function(x, re) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	73 matches <- regexpr(re,x,perl=TRUE)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	74 start <- attr(matches,"capture.start")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	75 end <- start + attr(matches,"capture.length") - 1
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	76 do.call(cbind,lapply(1:ncol(start), function(i) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	77 sapply(1:nrow(start),function(j){
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	78 if (start[j,i] > -1) substr(x[[j]],start[j,i],end[j,i]) else NA
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	79 })
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	80 }))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	81 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	82
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	83 # ###
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	84 # # Function to globally excise regex groups from string vectors.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	85 # # x = string vector
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	86 # # re = regular expression with groups
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	87 # #
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	88 # global.extract.groups <- function(x,re) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	89 # all.matches <- gregexpr(re,x,perl=TRUE)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	90 # mapply(function(matches,x) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	91 # start <- attr(matches,"capture.start")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	92 # end <- start + attr(matches,"capture.length") - 1
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	93 # apply(zbind(start,end),c(1,2),function(pos) substr(x,pos[[1]],pos[[2]]) )
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	94 # },matches=all.matches,x=x,SIMPLIFY=FALSE)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	95 # }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	96
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	97 ###
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	98 # Helper function to split multi-mutant bodies into their individual
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	99 # elements. Returns a vector of strings containing these elements.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	100 # An attribute "multi" is attached to the vector, detailing the type
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	101 # of multi-mutant
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	102 #
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	103 splitMulti <- function(body) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	104 if (regexpr("\\[.+\\];\\[.+\\]",body) > 0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	105 out <- strsplit(substr(body,2,nchar(body)-1),"\\];\\[")[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	106 attr(out,"multi") <- "trans"
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	107 } else if (regexpr("\\[.+\$;\$.+\\]",body) > 0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	108 out <- strsplit(substr(body,2,nchar(body)-1),"\$;\$")[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	109 attr(out,"multi") <- "unknown"
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	110 } else if (regexpr("\\[.+;.+\\]",body) > 0) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	111 out <- strsplit(substr(body,2,nchar(body)-1),";")[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	112 attr(out,"multi") <- "cis"
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	113 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	114 out <- body
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	115 attr(out,"multi") <- "single"
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 return(out)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	118 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	119
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	120 ###
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	121 # Helper function:
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	122 # Given an HGVS body and a list of regexes corresponding to types,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	123 # find the (first) matching type.
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	124 findType <- function(body,types) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	125 i <- 0
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	126 found <- done <- FALSE
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	127 while (!found && !done) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	128 found <- regexpr(types[[i <- i+1]],body) > 0
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	129 done <- i >= length(types)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	130 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	131 if (found) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	132 return(names(types)[[i]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	133 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	134 return("invalid")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	135 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	136 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	137
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	138 out <- lapply(strings,function(s) {
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 if (regexpr("^[gcnmrp]\\.",s) < 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	141 return(list(list(hgvs=s,subject="invalid",type="invalid")))
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 body <- substr(s,3,nchar(s))
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 subbodies <- splitMulti(body)
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 subjects <- c(
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	149 g="genomic",c="coding",n="noncoding",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	150 m="mitochondrial",r="rna",p="protein"
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	151 )
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	152 subject <- subjects[[substr(s,1,1)]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	153
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	154 if (subject=="genomic") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	155
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	156 types <- c(
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	157 substitution="\\d+[ACGT]>[ACGT]", singledeletion="^\\d+del$",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	158 deletion="\\d+_\\d+del$",inversion="\\d+_\\d+inv",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	159 duplication="\\d+_\\d+dup",insertion="\\d+_\\d+ins[ATCG]+",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	160 conversion="\\d+_\\d+con\\d+_\\d+",delins="\\d+_\\d+delins[ATCG]+",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	161 amplification="\\d+_\\d+\\[\\d+\\]"
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	162 )
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	163
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	164 phasing <- attr(subbodies,"multi")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	165 isMulti <- length(subbodies) > 1
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	166
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	167 lapply(1:length(subbodies), function(i.multi) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	168 body <- subbodies[[i.multi]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	169
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	170 type <- findType(body,types)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	171
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	172 if (type == "substitution") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	173 groups <- extract.groups(body,"(\\d+)([ACGT])>([ACGT])")[1,]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	174 position <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	175 ancestral <- groups[[2]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	176 variant <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	177 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	178 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	179 type=type,start=position,ancestral=ancestral,variant=variant))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	180 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	181 return(list(hgvs=s,subject=subject,type=type,start=position,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	182 ancestral=ancestral,variant=variant))
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 } else if (type == "singledeletion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	186 groups <- extract.groups(body,"(\\d+)del")[1,]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	187 position <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	188 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	189 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	190 type=type,start=position))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	191 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	192 return(list(hgvs=s,subject=subject,type=type,start=position))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	193 }
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 } else if (type == "deletion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	196 groups <- extract.groups(body,"(\\d+)_(\\d+)del")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	197 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	198 end <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	199 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	200 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	201 type=type,start=start,end=end))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	202 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	203 return(list(hgvs=s,subject=subject,type=type,start=start,end=end))
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 } else if (type == "inversion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	207 groups <- extract.groups(body,"(\\d+)_(\\d+)inv")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	208 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	209 end <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	210 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	211 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	212 type=type,start=start,end=end))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	213 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	214 return(list(hgvs=s,subject=subject,type=type,start=start,end=end))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	215 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	216
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	217 } else if (type == "duplication") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	218 groups <- extract.groups(body,"(\\d+)_(\\d+)dup")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	219 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	220 end <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	221 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	222 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	223 type=type,start=start,end=end))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	224 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	225 return(list(hgvs=s,subject=subject,type=type,start=start,end=end))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	226 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	227
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	228 } else if (type == "insertion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	229 groups <- extract.groups(body,"(\\d+)_(\\d+)ins([ATCG]+)")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	230 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	231 end <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	232 if (abs(end-start)!=1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	233 warning("Invalid insertion definition:
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	234 Start and end positions must be adjacent!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	235 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	236 variant <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	237 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	238 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	239 type=type,start=start,end=end,variant=variant))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	240 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	241 return(list(hgvs=s,subject=subject,type=type,start=start,end=end,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	242 variant=variant))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	243 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	244
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	245 } else if (type == "conversion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	246 groups <- extract.groups(body,"(\\d+)_(\\d+)con(\\d+)_(\\d+)")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	247 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	248 end <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	249 tStart <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	250 tEnd <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	251 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	252 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	253 type=type,start=start,end=end,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	254 templateStart=tStart,templateEnd=tEnd))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	255 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	256 return(list(hgvs=s,subject=subject,type=type,start=start,end=end,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	257 templateStart=tStart,templateEnd=tEnd))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	258 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	259
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	260 } else if (type == "delins") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	261 groups <- extract.groups(body,"(\\d+)_(\\d+)delins([ATCG]+)")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	262 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	263 end <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	264 variant <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	265 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	266 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	267 type=type,start=start,end=end,variant=variant))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	268 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	269 return(list(hgvs=s,subject=subject,type=type,start=start,end=end,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	270 variant=variant))
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
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	273 } else if (type == "amplification") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	274 groups <- extract.groups(body,"(\\d+)_(\\d+)\\[(\\d+)\\]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	275 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	276 end <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	277 copies <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	278 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	279 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	280 type=type,start=start,end=end,copies=copies))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	281 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	282 return(list(hgvs=s,subject=subject,type=type,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	283 start=start,end=end,copies=copies))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	284 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	285
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	286 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	287 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	288 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	289 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	290 return(list(hgvs=s,subject=subject,type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	291 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	292 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	293
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	294 })
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	295
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	296 } else if (subject=="coding") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	297 #coding needs to be handled separately from genomic, as the syntax may differ
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	298 #e.g. it allows for offset descriptions relative to exon-intron borders
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	299
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	300 types <- c(
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	301 substitution="\\d+([+-]\\d+)?[ACGT]>[ACGT]",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	302 singledeletion="^\\d+([+-]\\d+)?del$",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	303 deletion="\\d+([+-]\\d+)?_\\d+([+-]\\d+)?del$",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	304 inversion="\\d+([+-]\\d+)?_\\d+([+-]\\d+)?inv",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	305 duplication="\\d+([+-]\\d+)?_\\d+([+-]\\d+)?dup",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	306 insertion="\\d+([+-]\\d+)?_\\d+([+-]\\d+)?ins[ATCG]+",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	307 conversion="\\d+([+-]\\d+)?_\\d+([+-]\\d+)?con\\d+([+-]\\d+)?_\\d+([+-]\\d+)?",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	308 delins="\\d+([+-]\\d+)?_\\d+([+-]\\d+)?delins[ATCG]+",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	309 amplification="\\d+([+-]\\d+)?_\\d+([+-]\\d+)?\\[\\d+\\]"
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
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	312 phasing <- attr(subbodies,"multi")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	313 isMulti <- length(subbodies) > 1
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	314
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	315 lapply(1:length(subbodies), function(i.multi) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	316 body <- subbodies[[i.multi]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	317
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	318 type <- findType(body,types)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	319
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	320 if (type == "substitution") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	321 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?([ACGT])>([ACGT])")[1,]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	322 position <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	323 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	324 ancestral <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	325 variant <- groups[[4]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	326 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	327 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	328 type=type,start=position,startIntron=intronOffset,ancestral=ancestral,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	329 variant=variant))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	330 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	331 return(list(hgvs=s,subject=subject,type=type,start=position,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	332 startIntron=intronOffset,ancestral=ancestral,variant=variant))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	333 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	334
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	335 } else if (type == "singledeletion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	336 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?del")[1,]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	337 position <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	338 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	339 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	340 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	341 type=type,start=position,startIntron=intronOffset))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	342 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	343 return(list(hgvs=s,subject=subject,type=type,start=position,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	344 startIntron=intronOffset))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	345 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	346 } else if (type == "deletion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	347 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?_(\\d+)([+-]\\d+)?del")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	348 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	349 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	350 end <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	351 intronOffset2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	352 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	353 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	354 type=type,start=start,startIntron=intronOffset,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	355 end=end,endIntron=intronOffset2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	356 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	357 return(list(hgvs=s,subject=subject,type=type,start=start,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	358 startIntron=intronOffset,end=end,endIntron=intronOffset2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	359 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	360 } else if (type == "inversion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	361 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?_(\\d+)([+-]\\d+)?inv")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	362 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	363 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	364 end <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	365 intronOffset2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	366 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	367 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	368 type=type,start=start,startIntron=intronOffset,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	369 end=end,endIntron=intronOffset2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	370 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	371 return(list(hgvs=s,subject=subject,type=type,start=start,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	372 startIntron=intronOffset,end=end,endIntron=intronOffset2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	373 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	374 } else if (type == "duplication") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	375 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?_(\\d+)([+-]\\d+)?dup")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	376 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	377 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	378 end <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	379 intronOffset2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	380 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	381 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	382 type=type,start=start,startIntron=intronOffset,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	383 end=end,endIntron=intronOffset2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	384 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	385 return(list(hgvs=s,subject=subject,type=type,start=start,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	386 startIntron=intronOffset,end=end,endIntron=intronOffset2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	387 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	388 } else if (type == "insertion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	389 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?_(\\d+)([+-]\\d+)?ins([ATCG]+)")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	390 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	391 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	392 end <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	393 intronOffset2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	394 variant <- groups[[5]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	395 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	396 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	397 type=type,start=start,startIntron=intronOffset,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	398 end=end,endIntron=intronOffset2,variant=variant))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	399 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	400 return(list(hgvs=s,subject=subject,type=type,start=start,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	401 startIntron=intronOffset,end=end,endIntron=intronOffset2,variant=variant))
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 } else if (type == "conversion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	404 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?_(\\d+)([+-]\\d+)?con(\\d+)([+-]\\d+)?_(\\d+)([+-]\\d+)?")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	405 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	406 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	407 end <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	408 intronOffset2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	409 tStart <- as.integer(groups[[5]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	410 intronOffset3 <- as.integer(groups[[6]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	411 tEnd <- as.integer(groups[[7]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	412 intronOffset4 <- as.integer(groups[[8]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	413 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	414 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	415 type=type,start=start,startIntron=intronOffset,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	416 end=end,endIntron=intronOffset2,templateStart=tStart,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	417 templateStartIntron=intronOffset3,templateEnd=tEnd,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	418 templateEndIntron=intronOffset4))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	419 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	420 return(list(hgvs=s,subject=subject,type=type,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	421 start=start,startIntron=intronOffset,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	422 end=end,endIntron=intronOffset2,templateStart=tStart,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	423 templateStartIntron=intronOffset3,templateEnd=tEnd,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	424 templateEndIntron=intronOffset4))
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 } else if (type == "delins") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	427 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?_(\\d+)([+-]\\d+)?delins([ATCG]+)")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	428 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	429 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	430 end <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	431 intronOffset2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	432 variant <- groups[[5]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	433 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	434 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	435 type=type,start=start,startIntron=intronOffset,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	436 end=end,endIntron=intronOffset2,variant=variant))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	437 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	438 return(list(hgvs=s,subject=subject,type=type,start=start,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	439 startIntron=intronOffset,end=end,endIntron=intronOffset2,variant=variant))
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 } else if (type == "amplification") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	442 groups <- extract.groups(body,"(\\d+)([+-]\\d+)?_(\\d+)([+-]\\d+)?\\[(\\d+)\\]")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	443 start <- as.integer(groups[[1]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	444 intronOffset <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	445 end <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	446 intronOffset2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	447 copies <- as.integer(groups[[3]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	448 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	449 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	450 type=type,start=start,startIntron=intronOffset,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	451 end=end,endIntron=intronOffset2,copies=copies))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	452 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	453 return(list(hgvs=s,subject=subject,type=type,start=start,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	454 startIntron=intronOffset,end=end,endIntron=intronOffset2,copies=copies))
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 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	457 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	458 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	459 type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	460 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	461 return(list(hgvs=s,subject=subject,type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	462 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	463 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	464
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	465 })
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	466
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	467 } else if (subject=="protein") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	468
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	469 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	470 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	471 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	472 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	473 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	474 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	475 codes <- paste(c(one2three,three2one[-21],"\\*"),collapse="\|")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	476
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	477 types <- list(
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	478 synonymous1="^=$",
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	479 synonymous2=paste0("^(",codes,")(\\d+)=$"),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	480 substitution=paste0("^(",codes,")(\\d+)(",codes,")$"),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	481 singledeletion=paste0("^(",codes,")(\\d+)del$"),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	482 deletion=paste0("^(",codes,")(\\d+)_(",codes,")(\\d+)del$"),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	483 duplication=paste0("^(",codes,")(\\d+)_(",codes,")(\\d+)dup$"),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	484 insertion=paste0("^(",codes,")(\\d+)_(",codes,")(\\d+)ins((",codes,")+)$"),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	485 delins=paste0("^(",codes,")(\\d+)_(",codes,")(\\d+)delins((",codes,")+)$"),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	486 frameshift1=paste0("^(",codes,")(\\d+)fs$"),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	487 frameshift2=paste0("^(",codes,")(\\d+)(",codes,")fs(Ter\|\\*)(\\d+)$")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	488 )
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 phasing <- attr(subbodies,"multi")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	491 isMulti <- length(subbodies) > 1
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 lapply(1:length(subbodies), function(i.multi) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	494 body <- subbodies[[i.multi]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	495
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	496 type <- findType(body,types)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	497
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	498 if (type == "synonymous1") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	499 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	500 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,type=type))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	501 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	502 return(list(hgvs=s,subject=subject,type="synonymous"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	503 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	504 } else if (type == "synonymous2") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	505 groups <- extract.groups(body,types$synonymous2)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	506 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	507 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	508 if (aa1 %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	509 if (is.na(aacode)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	510 #do nothing
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	511 } else if (aacode == 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	512 if (nchar(aa1) == 3) aa1 <- three2one[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	513 } else if (aacode ==3) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	514 if (nchar(aa1) == 1) aa1 <- one2three[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	515 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	516 #this should never happen, as it's supposed to be detected at start of function
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	517 stop("Invalid aacode. If you see this, report this as a bug!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	518 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	519 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	520 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	521 type="synonymous",start=pos,ancestral=aa1))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	522 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	523 return(list(hgvs=s,subject=subject,type="synonymous",start=pos,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	524 ancestral=aa1))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	525 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	526 } else {#not valid amino acid
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	527 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	528 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	529 type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	530 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	531 return(list(hgvs=s,subject=subject,type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	532 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	533 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	534 } else if (type == "substitution") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	535 groups <- extract.groups(body,types$substitution)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	536 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	537 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	538 aa2 <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	539 if (aa1 %in% c(one2three,three2one) && aa2 %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	540 if (is.na(aacode)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	541 #do nothing
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	542 } else if (aacode == 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	543 if (nchar(aa1) == 3) aa1 <- three2one[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	544 if (nchar(aa2) == 3) aa2 <- three2one[[aa2]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	545 } else if (aacode ==3) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	546 if (nchar(aa1) == 1) aa1 <- one2three[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	547 if (nchar(aa2) == 1) aa2 <- one2three[[aa2]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	548 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	549 #this should never happen, as it's supposed to be detected at start of function
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	550 stop("Invalid aacode. If you see this, report this as a bug!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	551 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	552 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	553 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	554 type=type,start=pos,ancestral=aa1,variant=aa2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	555 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	556 return(list(hgvs=s,subject=subject,type=type,start=pos,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	557 ancestral=aa1,variant=aa2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	558 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	559 } else {#not valid amino acid
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	560 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	561 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	562 type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	563 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	564 return(list(hgvs=s,subject=subject,type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	565 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	566 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	567
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	568 } else if (type == "singledeletion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	569 groups <- extract.groups(body,types$singledeletion)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	570 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	571 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	572 if (is.na(aacode)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	573 #do nothing
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	574 } else if (aacode == 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	575 if (nchar(aa1) == 3) aa1 <- three2one[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	576 } else if (aacode == 3) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	577 if (nchar(aa1) == 1) aa1 <- one2three[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	578 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	579 #this should never happen, as it's supposed to be detected at start of function
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	580 stop("Invalid aacode. If you see this, report this as a bug!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	581 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	582 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	583 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	584 type=type,start=pos,ancestral=aa1))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	585 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	586 return(list(hgvs=s,subject=subject,type=type,start=pos,ancestral=aa1))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	587 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	588 } else if (type == "deletion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	589 groups <- extract.groups(body,types$deletion)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	590 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	591 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	592 aa2 <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	593 pos2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	594 if (is.na(aacode)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	595 #do nothing
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	596 } else if (aacode == 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	597 if (nchar(aa1) == 3) aa1 <- three2one[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	598 if (nchar(aa2) == 3) aa2 <- three2one[[aa2]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	599 } else if (aacode == 3) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	600 if (nchar(aa1) == 1) aa1 <- one2three[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	601 if (nchar(aa2) == 1) aa2 <- one2three[[aa2]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	602 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	603 #this should never happen, as it's supposed to be detected at start of function
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	604 stop("Invalid aacode. If you see this, report this as a bug!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	605 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	606 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	607 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	608 type=type,start=pos,ancestral=aa1,end=pos2,ancestral2=aa2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	609 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	610 return(list(hgvs=s,subject=subject,type=type,start=pos,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	611 ancestral=aa1,end=pos2,ancestral2=aa2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	612 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	613
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	614 } else if (type == "duplication") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	615 groups <- extract.groups(body,types$duplication)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	616 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	617 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	618 aa2 <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	619 pos2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	620 if (is.na(aacode)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	621 #do nothing
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	622 } else if (aacode == 1) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	623 if (nchar(aa1) == 3) aa1 <- three2one[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	624 if (nchar(aa2) == 3) aa2 <- three2one[[aa2]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	625 } else if (aacode == 3) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	626 if (nchar(aa1) == 1) aa1 <- one2three[[aa1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	627 if (nchar(aa2) == 1) aa2 <- one2three[[aa2]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	628 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	629 #this should never happen, as it's supposed to be detected at start of function
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	630 stop("Invalid aacode. If you see this, report this as a bug!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	631 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	632 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	633 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	634 type=type,start=pos,ancestral=aa1,end=pos2,ancestral2=aa2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	635 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	636 return(list(hgvs=s,subject=subject,type=type,start=pos,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	637 ancestral=aa1,end=pos2,ancestral2=aa2))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	638 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	639
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	640 } else if (type == "insertion") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	641 groups <- extract.groups(body,types$insertion)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	642 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	643 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	644 aa2 <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	645 pos2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	646 insert <- groups[[5]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	647 #TODO: Implement code conversion
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	648 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	649 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	650 type=type,start=pos,ancestral=aa1,end=pos2,ancestral2=aa2,variant=insert))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	651 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	652 return(list(hgvs=s,subject=subject,type=type,start=pos,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	653 ancestral=aa1,end=pos2,ancestral2=aa2,variant=insert))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	654 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	655
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	656 } else if (type == "delins") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	657 groups <- extract.groups(body,types$delins)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	658 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	659 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	660 aa2 <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	661 pos2 <- as.integer(groups[[4]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	662 insert <- groups[[5]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	663 #TODO: Implement code conversion
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	664 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	665 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	666 type=type,start=pos,ancestral=aa1,end=pos2,ancestral2=aa2,variant=insert))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	667 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	668 return(list(hgvs=s,subject=subject,type=type,start=pos,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	669 ancestral=aa1,end=pos2,ancestral2=aa2,variant=insert))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	670 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	671
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	672 } else if (type == "frameshift1") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	673 groups <- extract.groups(body,types$frameshift1)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	674 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	675 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	676 #TODO: Implement code conversion
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	677 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	678 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	679 type="frameshift",start=pos,ancestral=aa1))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	680 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	681 return(list(hgvs=s,subject=subject,type="frameshift",start=pos,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	682 ancestral=aa1))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	683 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	684
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	685 } else if (type == "frameshift2") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	686 groups <- extract.groups(body,types$frameshift2)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	687 aa1 <- groups[[1]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	688 pos <- as.integer(groups[[2]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	689 aa2 <- groups[[3]]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	690 term <- as.integer(groups[[5]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	691 #TODO: Implement code conversion
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	692 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	693 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	694 type="frameshift",start=pos,ancestral=aa1,variant=aa2,end=term))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	695 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	696 return(list(hgvs=s,subject=subject,type="frameshift",start=pos,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	697 ancestral=aa1,variant=aa2,end=term))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	698 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	699
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	700 } else {#unmatched type
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	701 if (isMulti) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	702 return(list(hgvs=s,subject=subject,phasing=phasing,multiPart=i.multi,
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	703 type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	704 } else {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	705 return(list(hgvs=s,subject=subject,type="invalid"))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	706 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	707 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	708
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	709 })
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	710
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	711 } else if (subject=="noncoding") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	712 #FIXME: These need to be list of lists to match postprocessing
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	713 return(list(list(hgvs=s,subject="not_implemented",type="not_implemented")))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	714 } else if (subject=="mitochondrial") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	715 return(list(list(hgvs=s,subject="not_implemented",type="not_implemented")))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	716 } else if (subject=="rna") {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	717 return(list(list(hgvs=s,subject="not_implemented",type="not_implemented")))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	718 } else {#unmatched subject, shouldn't happen
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	719 stop("Unmatched subject! If you see this, report it as a bug!")
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	720 }
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	721 })
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	722
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	723 #demote multimutants to enforce simple list structure
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	724 multiLengths <- sapply(out,length)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	725 ids <- do.call(c,lapply(1:length(multiLengths),
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	726 function(i) if (multiLengths[[i]]==1) as.character(i) else paste0(i,".",1:multiLengths[[i]])
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	727 ))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	728 out2 <- do.call(c,out)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	729 names(out2) <- ids
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	730
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	731
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	732
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	733 to.df(out2)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0 iuc parents: diff changeset	734 }

Mercurial > repos > iuc > hgvsparser

annotate parseHGVS.R @ 0:c12a4d187121 draft default tip