diff get_expression_profiles.R @ 8:2c0bab71a436 draft

planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_expression_profiles.R	Tue Dec 18 09:48:29 2018 -0500
@@ -0,0 +1,146 @@
+# Read file and return file content as data.frame
+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)
+  }
+}
+
+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)
+  }
+}
+
+# input has to be a list of IDs in ENSG format
+# tissue is one of unique(HPA.normal.tissue$Tissue)
+# level is one, or several, or 0 (=ALL) of "Not detected", "Medium", "High", "Low"
+# reliability is one, or several, or 0 (=ALL) of "Approved", "Supported", "Uncertain"
+annot.HPAnorm<-function(input, HPA_normal_tissue, tissue, level, reliability, not_mapped_option) {
+  dat <- subset(HPA_normal_tissue, Gene %in% input)
+  res.Tissue<-subset(dat, Tissue %in% tissue) 
+  res.Level<-subset(res.Tissue, Level %in% level) 
+  res.Rel<-subset(res.Level, Reliability %in% reliability) 
+  
+  if (not_mapped_option) {
+    if (length(setdiff(intersect(input, unique(dat$Gene)), unique(res.Rel$Gene)))>0) {
+      not_match_IDs <- matrix(setdiff(intersect(input, unique(dat$Gene)), unique(res.Rel$Gene)), ncol = 1, nrow = length(setdiff(intersect(input, unique(dat$Gene)), unique(res.Rel$Gene))))
+      not.match <- matrix("no match", ncol = ncol(HPA_normal_tissue) - 1, nrow = length(not_match_IDs))
+      not.match <- cbind(not_match_IDs, unname(not.match))
+      colnames(not.match) <- colnames(HPA_normal_tissue)
+      res <- rbind(res.Rel, not.match)
+    } else {
+      res <- res.Rel
+    } 
+    
+    if (length(setdiff(input, unique(dat$Gene)))>0) {
+      not.mapped <- matrix(ncol = ncol(HPA_normal_tissue) - 1, nrow = length(setdiff(input, unique(dat$Gene))))
+      not.mapped <- cbind(matrix(setdiff(input, unique(dat$Gene)), ncol = 1, nrow = length(setdiff(input, unique(dat$Gene)))), unname(not.mapped))
+      colnames(not.mapped) <- colnames(HPA_normal_tissue)
+      res <- rbind(res, not.mapped)
+    }
+    
+  } else {
+    res <- res.Rel
+  }
+  
+  return(res)
+  
+}
+
+annot.HPAcancer<-function(input, HPA_cancer_tissue, cancer, not_mapped_option) {
+  dat <- subset(HPA_cancer_tissue, Gene %in% input)
+  res.Cancer<-subset(dat, Cancer %in% cancer) 
+
+  if (not_mapped_option) {
+    not.mapped <- matrix(ncol=ncol(HPA_cancer_tissue)-1, nrow=length(setdiff(input, unique(dat$Gene))))
+    not.mapped <- cbind(matrix(setdiff(input, unique(dat$Gene)), ncol = 1, nrow = length(setdiff(input, unique(dat$Gene)))), unname(not.mapped))
+    colnames(not.mapped) <- colnames(HPA_cancer_tissue)
+    res <- rbind(res.Cancer, not.mapped)
+  } else {
+    res <- res.Cancer
+  }
+  return(res)
+}
+
+
+main <- function() {
+  args <- commandArgs(TRUE)
+  if(length(args)<1) {
+    args <- c("--help")
+  }
+  
+  # Help section
+  if("--help" %in% args) {
+    cat("Selection and Annotation HPA
+    Arguments:
+        --ref_file: HPA normal/cancer tissue file path
+        --input_type: type of input (list of id or filename)
+        --input: list of IDs in ENSG format
+        --column_number: the column number which you would like to apply...
+        --header: true/false if your file contains a header
+        --atlas: normal/cancer
+          if normal:
+            --tissue: list of tissues
+            --level: Not detected, Low, Medium, High
+            --reliability: Supportive, Uncertain
+          if cancer:
+            --cancer: Cancer tissues
+        --not_mapped: true/false if your output file should contain not-mapped and not-match IDs 
+        --output: output filename \n")
+    q(save="no")
+  }
+  
+  # Parse arguments
+  parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
+  argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
+  args <- as.list(as.character(argsDF$V2))
+  names(args) <- argsDF$V1
+  
+  #save(args,file = "/home/dchristiany/proteore_project/ProteoRE/tools/Get_expression_profiles/args.rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/Get_expression_profiles/args.rda")
+  
+  # Extract input
+  input_type = args$input_type
+  if (input_type == "list") {
+    list_id = strsplit(args$input, "[ \t\n]+")[[1]]
+  } else if (input_type == "file") {
+    filename = args$input
+    column_number = as.numeric(gsub("c", "" ,args$column_number))
+    header = str2bool(args$header)
+    file = read_file(filename, header)
+    list_id = sapply(strsplit(file[,column_number], ";"), "[", 1)
+  }
+  input = list_id
+
+  # Read reference file
+  reference_file = read_file(args$ref_file, TRUE)
+
+  # Extract other options
+  atlas = args$atlas
+  not_mapped_option = str2bool(args$not_mapped)
+  if (atlas=="normal") {
+    tissue = strsplit(args$tissue, ",")[[1]]
+    level = strsplit(args$level, ",")[[1]]
+    reliability = strsplit(args$reliability, ",")[[1]]
+    # Calculation
+    res = annot.HPAnorm(input, reference_file, tissue, level, reliability, not_mapped_option)
+  } else if (atlas=="cancer") {
+    cancer = strsplit(args$cancer, ",")[[1]]
+    # Calculation
+    res = annot.HPAcancer(input, reference_file, cancer, not_mapped_option)
+  }
+  
+  # Write output
+  output = args$output
+  res <- apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x))
+  write.table(res, output, sep = "\t", quote = FALSE, row.names = FALSE)
+}
+
+main()