R/amelioration-annotation.R

In maous1/Syngulon: analyse bacteria genome

#' Fonction qui retire les underscore dans la colonne gene des annotation
#'
#' @param species espece consernée
#' @param collicin les gènes consernés
#' @param annotationDir la localisation des fichiers d'annotations
#'
#' @return
#' @export

amelioration.annotation <- function(species,collicin,annotationDir){
  library(dplyr)

  collicin <- collicin$genename
  collicin <- toupper(collicin)
  annotationfiles <- list.files(annotationDir,full.names = T,recursive = T)


  for(i in 1:length(annotationfiles))
  {
    currentfile <- read.csv(annotationfiles[i])
    currentfile$gene <- unlist(lapply(strsplit(currentfile$gene,split='_'),function(x) x[[1]]))
    write.csv(currentfile,annotationfiles[i])
    print(i)
  }


  ####### un debut pour extraire les produits des genes et les analyser
  #for (i in 1:length(collicin)) {
  #product <-c()
  #for (j in 1:length(annotationfiles)) {
  # currentfile <- read.csv(annotationfiles[j])
  #currentfile$gene <- toupper(currentfile$gene)
  #currentfile <- currentfile%>%filter(gene==collicin[i])
  #product <- c(product,currentfile$product)
  #}
  #print(i)
  #write.csv(table(product),paste0("99-results/","table.",collicin[i],".csv"))
  #}

}