#' Create accession csv file à la base du package genome. il sort les accessions numbers des chromosomes
#'
#' @param species a vector of character including the species that we want to analyze
#' @param bacteria.table The bacteria table produced by the create.bacteria.table function
#' @param outDir The output directory
#'
#' @return
#' @export
#'
#' @examples
download.accession.chromosome <- function(species,bacteria.table,outDir)
{
library(reutils)
library(ape)
library(seqinr)
library(Biostrings)
library(dplyr)
library(WriteXLS)
bacteria.table$Replicons <- unlist(lapply(strsplit(bacteria.table$Replicons,split='plasmid'),function(x) x[1]))
n.species <- length(species)
for(i in 1:n.species)
{
data1species <- bacteria.table[bacteria.table$Organism==species[i],]
data1species <- data1species[is.na(data1species$Replicons)==F,]
Nstrains <- dim(data1species)[1]
Replicon.vec <- NULL
for(j in 1:Nstrains)
{
Replicon <- data1species$Replicons[j]
Replicon <- strsplit(Replicon,split=';')[[1]]
Replicon <- Replicon[grep(':',Replicon)]
Replicon <- unlist(lapply(strsplit(Replicon,split=':'), function(x) x[[2]]))
Replicon <- unlist(lapply(strsplit(Replicon,split='/'), function(x) x[[1]]))
Replicon <- gsub(Replicon,pattern = ' ',replacement = '')
Replicon <- paste(Replicon,collapse = " - ")
Replicon.vec <- c(Replicon.vec,Replicon)
}
accession <- data.frame(accession=Replicon.vec)
write.csv(accession,paste0(outDir,species[i],'.csv'),row.names = F)
}
}
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