diff sel_ann_hpa.R @ 0:5501e74891e4 draft

planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sel_ann_hpa.R	Fri Feb 16 04:22:54 2018 -0500
@@ -0,0 +1,179 @@
+
+# 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)
+    #Read the data of the files (skipping the first row):
+    file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
+    # Remove empty rows
+    #file <- file[!apply(is.na(file) | file == "", 1, all),]
+    #And assign the header to the data:
+    names(file) <- headers
+  }
+  else {
+    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
+  }
+  return(file)
+}
+
+
+# input has to be a list of IDs in ENSG format
+# tissue is one of unique(HPA.normal.tissue$Tissue)
+# level is one, or several, or 0 (=ALL) of "Not detected", "Medium", "High", "Low"
+# reliability is one, or several, or 0 (=ALL) of "Approved", "Supported", "Uncertain"
+annot.HPAnorm<-function(input, HPA_normal_tissue, tissue, level, reliability, not_mapped_option) {
+  dat <- subset(HPA_normal_tissue, Gene %in% input)
+  
+  if (length(tissue)==1) { 
+    res.Tissue<-subset(dat, Tissue==tissue) 
+  }
+  if (length(tissue)>1)  { 
+    res.Tissue<-subset(dat, Tissue %in% tissue) 
+  }
+  
+  if (length(level)==1) { 
+    res.Level<-subset(res.Tissue, Level==level) 
+  }
+  if (length(level)>1)  { 
+    print(level)
+    res.Level<-subset(res.Tissue, Level %in% level) 
+  }
+  
+  if (length(reliability)==1) { 
+    res.Rel<-subset(res.Level, Reliability==reliability) 
+  }
+  if (length(reliability)>1)  {
+    print(reliability)
+    res.Rel<-subset(res.Level, Reliability %in% reliability) 
+  }
+  
+  if (not_mapped_option == "true") {
+    if (length(setdiff(intersect(input, unique(dat$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$Gene))))
+      not.match <- matrix("not match", ncol = ncol(HPA_normal_tissue) - 1, nrow = length(not_match_IDs))
+      not.match <- cbind(not_match_IDs, unname(not.match))
+      colnames(not.match) <- colnames(HPA_normal_tissue)
+      res <- rbind(res.Rel, not.match)
+    }
+    else {
+      res <- res.Rel
+    }
+    if (length(setdiff(input, unique(dat$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$Gene)))), unname(not.mapped))
+      colnames(not.mapped) <- colnames(HPA_normal_tissue)
+      res <- rbind(res, not.mapped)
+    }
+  }
+  else {
+    res <- res.Rel
+  }
+  
+  return(res)
+  
+}
+
+annot.HPAcancer<-function(input, HPA_cancer_tissue, cancer, not_mapped_option) {
+  dat <- subset(HPA_cancer_tissue, Gene %in% input)
+
+  if (length(cancer)==1) { 
+    res.Cancer<-subset(dat, Cancer==cancer) 
+  }
+  if (length(cancer)>1)  { 
+    res.Cancer<-subset(dat, Cancer %in% cancer) 
+  }
+
+  if (not_mapped_option == "true") {
+    not.mapped <- matrix(ncol=ncol(HPA_cancer_tissue)-1, nrow=length(setdiff(input, unique(dat$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
+  
+  # Extract input
+  input_type = args$input_type
+  if (input_type == "list") {
+    list_id = strsplit(args$input, " ")[[1]]
+  }
+  else if (input_type == "file") {
+    filename = args$input
+    column_number = as.numeric(gsub("c", "" ,args$column_number))
+    header = args$header
+    file = readfile(filename, header)
+    list_id = c()
+    print(file)
+    list_id = sapply(strsplit(file[,column_number], ";"), "[", 1)
+  }
+  input = list_id
+
+  # Read reference file
+  reference_file = read.table(args$ref_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
+  print(colnames(reference_file))
+
+  # Extract other options
+  atlas = args$atlas
+  not_mapped_option = args$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
+  write.table(res, output, sep = "\t", quote = FALSE, row.names = FALSE)
+}
+
+main()
+
+# Example commands
+# Rscript sel_ann_hpa.R --input_type="file" --input="./test-data/ENSGid.txt" --ref_file="./pathology.tsv" --cancer="lung cancer,carcinoid" --not_mapped="true" --column_number="c1" --header="true" --output="test-data/ENSG_tissue_output_cancer.txt"
+# Rscript sel_ann_hpa.R --input_type="file" --input="./test-data/ENSGid.txt" --ref_file="./normal_tissue.tsv" --tissue="lung" --level="Not detected,Medium,High,Low" --reliability="Approved,Supported,Uncertain" --column_number="c1" --header="true" --not_mapped="false" --output="./test-data/ENSG_tissue_output.txt"
+# Rscript sel_ann_hpa.R --input_type="file" --input="./test-data/ENSG_no_not_match.txt" --ref_file="/Users/LinCun/Documents/ProteoRE/usecase1/normal_tissue.csv" --tissue="lung" --level="Not detected,Medium,High,Low" --reliability="Approved,Supportive,Uncertain" --column_number="c1" --header="true" --output="./test-data/ENSG_tissue_output2.txt"
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