diff add_expression_HPA.R @ 9:5c260bd3552e draft

planemo upload commit eb7450f36863f02f036cbc52bf5525d68f22bd9e

--- a/add_expression_HPA.R	Fri Mar 23 10:31:59 2018 -0400
+++ b/add_expression_HPA.R	Tue Dec 18 08:23:48 2018 -0500
@@ -1,40 +1,94 @@
 # Read file and return file content as data.frame
-readfile = function(filename, header) {
-  if (header == "true") {
-    # Read only first line of the file as header:
-    headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "")
-    #Read the data of the files (skipping the first row)
-    file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "")
-    # Remove empty rows
-    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
-    #And assign the header to the data
-    names(file) <- headers
+read_file <- function(path,header){
+  file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE)
+  if (inherits(file,"try-error")){
+    stop("File not found !")
+  }else{
+    return(file)
   }
-  else {
-    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "")
-    # Remove empty rows
-    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
+}
+
+#convert a string to boolean
+str2bool <- function(x){
+  if (any(is.element(c("t","true"),tolower(x)))){
+    return (TRUE)
+  }else if (any(is.element(c("f","false"),tolower(x)))){
+    return (FALSE)
+  }else{
+    return(NULL)
   }
-  return(file)
 }
 
 add_expression = function(input, atlas, options) {
+  input <- unique(input[!is.na(input)])
+  input <- gsub("[[:blank:]]|\u00A0","",input)
   if (all(!input %in% atlas$Ensembl)) {
     return(NULL)
-  }
-  else {
-    res = matrix(nrow=length(input), ncol=0)
-    names = c()
-    for (opt in options) {
-      names = c(names, opt)
-      info = atlas[match(input, atlas$Ensembl,incomparable="NA"),][opt][,]
-      res = cbind(res, info)
-    }
-    colnames(res) = names
+  } else {
+    res = atlas[match(input,atlas$Ensembl),c("Ensembl",options)]
+    res = res[which(!is.na(res[,1])),]
+    row.names(res)=res[,1]
+    res=res[2:ncol(res)]
+    res <- as.data.frame(apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
     return(res)
   }
 }
 
+order_columns <- function (df,ncol){
+  if (ncol==1){ #already at the right position
+    return (df)
+  } else {
+    df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])]
+  }
+  return (df)
+}
+
+#take data frame, return  data frame
+split_ids_per_line <- function(line,ncol){
+  
+  #print (line)
+  header = colnames(line)
+  line[ncol] = gsub("[[:blank:]]","",line[ncol])
+  
+  if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
+    if (length(line)==1 ) {
+      lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
+    } else {
+      if (ncol==1) {                                #first column
+        lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
+      } else if (ncol==length(line)) {                 #last column
+        lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
+      } else {
+        lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)]))
+      }
+    }
+    colnames(lines)=header
+    return(lines)
+  } else {
+    return(line)
+  }
+}
+
+#create new lines if there's more than one id per cell in the columns in order to have only one id per line
+one_id_one_line <-function(tab,ncol){
+  
+  if (ncol(tab)>1){
+    
+    tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
+    header=colnames(tab)
+    res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
+    for (i in 1:nrow(tab) ) {
+      lines = split_ids_per_line(tab[i,],ncol)
+      res = rbind(res,lines)
+    }
+  }else {
+    res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
+    res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
+    colnames(res)=colnames(tab)
+  }
+  return(res)
+}
+
 main = function() {
   args <- commandArgs(TRUE)
   if(length(args)<1) {
@@ -63,59 +117,52 @@
   args <- as.list(as.character(argsDF$V2))
   names(args) <- argsDF$V1
 
+  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
+  
   inputtype = args$inputtype
   if (inputtype == "copypaste") {
     input = strsplit(args$input, "[ \t\n]+")[[1]]
-  }
-  else if (inputtype == "tabfile") {
+  } else if (inputtype == "tabfile") {
     filename = args$input
     ncol = args$column
     # Check ncol
     if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
       stop("Please enter an integer for level")
-    }
-    else {
+    } else {
       ncol = as.numeric(gsub("c", "", ncol))
     }
-    header = args$header
-    # Get file content
-    file = readfile(filename, header)
-    # Extract Protein IDs list
-    input = c()
-    for (row in as.character(file[,ncol])) {
-      input = c(input, strsplit(row, ";")[[1]][1])
-    }
+    header = str2bool(args$header)
+    file = read_file(filename, header)
+    file = one_id_one_line(file,ncol)
+    input = unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
+    input = input[which(!is.na(input))]
   }
 
   # Read protein atlas
   protein_atlas = args$atlas
-  protein_atlas = readfile(protein_atlas, "true")
+  protein_atlas = read_file(protein_atlas, T)
 
   # Add expression
   output = args$output
-  names = c()
   options = strsplit(args$select, ",")[[1]]
   res = add_expression(input, protein_atlas, options)
-
+  
   # Write output
   if (is.null(res)) {
     write.table("None of the input ENSG ids are can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
-  }
-  else {
+  } else {
     if (inputtype == "copypaste") {
-      names = c("Ensembl", colnames(res))
-      res = cbind(as.matrix(input), res)
-      colnames(res) = names
-      write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE)
+      input <- data.frame(input)
+      output_content = merge(input,res,by.x=1,by.y="row.names",incomparables = NA, all.x=T)
+      colnames(output_content)[1] = "Ensembl"
+    } else if (inputtype == "tabfile") {
+      output_content = merge(file, res, by.x=ncol, by.y="row.names", incomparables = NA, all.x=T)
+      output_content = order_columns(output_content,ncol)
     }
-    else if (inputtype == "tabfile") {
-      names = c(names(file), colnames(res))
-      output_content = cbind(file, res)
-      colnames(output_content) = names
-      write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
-    }
+  output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))
+  write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
   }
-
 }
 
 main()