writeFasta<-function(data, filename){
  fastaLines = c()
  for (rowNum in 1:nrow(data)){
    fastaLines = c(fastaLines, as.character(paste(">", data[rowNum,"name"], sep = "")))
    fastaLines = c(fastaLines,as.character(data[rowNum,"seq"]))
  }
  fileConn<-file(filename)
  writeLines(fastaLines, fileConn)
  close(fileConn)
}

library(seqinr)
for (x in c(1:nrow(strain.prot.concat))) { 
  prot.pop <- strain.prot.concat[x,]
  prot.pop.t <- data.frame(t(prot.pop),stringsAsFactors = F)
  prot.pop.t$name <- rownames(prot.pop.t)
  prot.pop.t <- prot.pop.t[-1,]
  colnames(prot.pop.t) <- c("seq","name")
  rownames(prot.pop.t) <- NULL
  prot.pop.t.x <- data.frame(lapply(prot.pop.t, function(x) gsub("\\*$","",x)), stringsAsFactors = FALSE) #remove the terminal "*" from each sequence
  prot.pop.t.x2 <- prot.pop.t.x[!(grepl("\\*",prot.pop.t.x$seq)==TRUE),] #delete rows with seqs that contain internal stop codons
  prot.pop.t.x3 <- prot.pop.t.x2[!is.na(prot.pop.t.x2$seq)==TRUE,] #delete rows with missing sequences
  writeFasta(prot.pop.t.x3, paste("proteins/",strain.prot.concat[x,1],sep=""))
}

library(Biostrings)
library(dplyr)
proteins <- list.files("strain.genes/")
strain.prot.concat <- prot.template
for (x in c(1:length(proteins))) {
  strain <- Biostrings::readAAStringSet(paste("strain.genes/",proteins[x],sep=""))
  gene <- names(strain)
  sequence <- paste(strain)
  strain <- data.frame(gene,sequence,stringsAsFactors = F)
  strain <- unique(strain) #for unclear reasons, a small subset of genes and sequences is duplicated; must remove duplicates
  strain <- strain[!duplicated(strain$gene),] #there is a tiny minority of genes which are split, two different seqs for a gene, this creates exponential havoc in the loop
  strain.prot.concat <- dplyr::left_join(strain.prot.concat, strain, by = "gene")
  colnames(strain.prot.concat)[2+x] <- gsub("\\.fa","",paste(proteins[x]))
}

strain.prot.concat <- strain.prot.concat[-2] #remove a dummy column

library(seqinr)
for (x in c(1:nrow(strain.prot.concat))) { 
  prot.pop <- strain.prot.concat[x,]
  prot.pop.t <- data.frame(t(prot.pop),stringsAsFactors = F)
  prot.pop.t$name <- rownames(prot.pop.t)
  prot.pop.t <- prot.pop.t[-1,]
  colnames(prot.pop.t) <- c("seq","name")
  rownames(prot.pop.t) <- NULL
  prot.pop.t.x <- data.frame(lapply(prot.pop.t, function(x) gsub("\\*$","",x)), stringsAsFactors = FALSE) #remove the terminal "*" from each sequence
  prot.pop.t.x2 <- prot.pop.t.x[!(grepl("\\*",prot.pop.t.x$seq)==TRUE),] #delete rows with seqs that contain internal stop codons
  prot.pop.t.x3 <- prot.pop.t.x2[!is.na(prot.pop.t.x2$seq)==TRUE,] #delete rows with missing sequences
  writeFasta(prot.pop.t.x3, paste("genes/",strain.prot.concat[x,1],sep=""))
}