R/readal.R

In helloicyvodka/ggVITA: An R package for VIsualization and annotation of Tree Alignment.

#' Read in the result of DELTA for analysis
#' @param outfile <Path of DELTA result>. Required.
#' @param fileS <TreeS file path>. Required.
#' @param fileT <TreeT file path>. Required.
#' @param cost  <Cost file path>. Required.
#' @param method <l or g>
#' @param max_target <target num for l>
#' @param test testNum
#' @param all <T or F>
#' @param prune pruneScore
#' @export


readal<-function(outfile,
                 fileS,
                 fileT,
                 cost,
                 method,
                 max.target=NULL,
                 test=NULL,
                 all=F,
                 prune=NULL
                 ){


  if(method=="l")DDD <- readal.alml(outfile,all=all)
  if(method=='g')DDD <- readal.almg(outfile,all=all)

   attr(DDD,"params") <- list(
                      outfile=outfile,
                      fileS=utils::read.table(fileS,header = T,colClasses = "character"),
                      fileT=utils::read.table(fileT,header = T,colClasses = "character"),
                      cost=cost,
                      method=method,
                      max.target=max.target,
                      test=test,
                      all=all,
                      prune=prune
                      )

   return(DDD)

}










































#-----------------------------------------------------------------------------------------------------

# #' Read in an alm file
# #'
# #' Read in an alm file and create a list accordingly
# #'
# #' An alm file contains the information of teriminal tips and their tissue types.
# #'
# #' @param fileS the address of the treeS alm file
# #' @param fileT the address of the treeT alm file
# #' @return NULL, but create a variable named "alm_label" automately
# #' @keywords readal.alm
# #' @import magrittr
# #' @export


# readal.alm<-function(fileS,fileT){
#
#   label_S<-read.table(fileS,header = T,colClasses = "character")
#
#   label_T<-read.table(fileT,header = T,colClasses = "character")
#
#
#   #
#
#
#   label_list_S<-list()
#
#   label_S$Lineage<-label_S$Lineage %>% as.character()
#
#   for(i in 1:nrow(label_S)){
#     label_list_S[[label_S[i,1]]]<-label_S[i,3]
#   }
#
#   #
#
#   label_list_T<-list()
#
#   label_T$Lineage<-label_T$Lineage %>% as.character()
#
#   for(i in 1:nrow(label_T)){
#     label_list_T[[label_T[i,1]]]<-label_T[i,3]
#   }
#
#   label_list<-list(treeS=label_list_S,treeT=label_list_T)
#
#   class(label_list)<-c("alm_list",class(label_list))
#
#   alm_label<-label_list
#
#   alm_label
#
#   #cat("The variable alm_label is created.")
#
# }

#------------------------------------------------------------------------------------------------------------------------










# #' Read local alignment results from HSA calculation and transform the result from txt to list in R
# #'
# #' @title readal.alml
# #' @author Meng Yuan
# #' @param file file address of alml result
# #' @return a list containing the result (phylos of treeS and treeT, the matching dataframe) and the result analysis (pValue and etc.)
# #' @export
# #' @import rlist
# #' @import plyr
# #' @import dplyr
# #' @import ggtree




# readal.alml<-function(file){
#
#   if(!exists("alm_label")){
#     stop("Please run readal.alm firstly and create the alm_label varaiable! ATTENTION: readal.alm will creates alm_label variable automately.")
#   }
#
#
#   the_result<-list()
#
#   the_prefix<-c("Score","RootS","RootT","PruneS","PruneT","MatchS","MatchT","}","PValue","Min")
#
#   the_text<-as.list(readLines(file))
#
#   nl<-length(the_text)
#
#
#
#   for(i in 1:nl-1){
#
#     the_line<-the_text[[i]]
#
#     if(regexpr("^[0-9]",the_line)){
#
#       num2<-as.integer(regmatches(the_line,regexpr("^([0-9]+)",the_line)))
#
#       if(length(num2)>0){
#
#         num<-as.character(regmatches(the_line,regexpr("^([0-9]+)",the_line)))
#
#         the_result[[num]]<-list()
#
#         the_result[[num]]<-list("score_order"=as.numeric(num))
#       }
#     }
#
#
#     for(i2 in 1:(length(the_prefix)-3)){
#
#       if(startsWith(the_line,the_prefix[i2])){
#
#         the_result[[num]][[as.character(the_prefix[i2])]]<-unlist(strsplit(the_line,split = ":"))[2]
#
#         }
#
#       }
#
#     if(startsWith(the_line,"PValue")){
#
#       the_result[["PValue"]][["all"]]<-unlist(strsplit(the_line,split = ":"))[2]
#
#       }
#
#     if(startsWith(the_line,"Min")){
#
#       the_result[["PValue"]][["Min"]]<-unlist(strsplit(unlist(strsplit(the_line,split = " "))[1],split = ":"))[2]
#
#       the_result[["PValue"]][["Max"]]<-unlist(strsplit(unlist(strsplit(the_line,split = " "))[2],split = ":"))[2]
#
#       the_result[["PValue"]][["AVG"]]<-unlist(strsplit(unlist(strsplit(the_line,split = " "))[3],split = ":"))[2]
#
#       }
#
#   }
#
#
#
#   # result_list<-lapply(the_result[1:(length(the_result)-1)],
#   #                     function(x){
#   #                       cat("=");
#   #                       return(alml_2_phylo(x))})
#
#
#   result_analysis<-strsplit(the_result[[length(the_result)]],split = " ")
#
#   the_pValue<-strsplit(result_analysis$all,split=" ") %>% unlist()
#
#   final_result<-list.update(the_result[-length(the_result)],PValue=as.numeric(the_pValue[.i]))
#
#   for(i in 1:length(final_result)){
#     class(final_result[[i]])<-c("alml",class(final_result[[i]]))
#   }
#
#   class(final_result)<-c("alml_list",class(final_result))
#
#   return(final_result)
#
#   }