#####################################################################################
# #
# Copyright (C) 2019 Jacob M. Wozniak #
# #
# This file is part of the PTMphinder R package. #
# #
# PTMphinder is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# any later version. #
# #
# PTMphinder is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with PTMphinder. If not, see <https://www.gnu.org/licenses/>. #
# #
#####################################################################################
extractBackground <- function(seqs, char, width){
library(stringr)
fullProt <- NULL
flankSeq <- NULL
flankList <- rep("",sum(str_count(seqs, char)))
halfWidth <- floor(width/2)
len<-length(seqs)
count <- 0
for(y in 1:len) {
fullProt <- seqs[y]
tempLoc <- gregexpr(pattern = char, fullProt)[[1]]
if(tempLoc[[1]]!=-1){
for(i in 1:length(tempLoc)){
count <- count + 1
flankSeq <- substr(fullProt, tempLoc[i]-halfWidth, tempLoc[i]+halfWidth)
flankList[count] <- flankSeq
}
}
fullProt <- NULL
tempLoc <- NULL
}
output <- unique(flankList[which(lapply(flankList, nchar)==width)])
return(output)
}
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