diff Get_ms-ms_observations.R @ 2:6ab9d2778f04 draft

planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Get_ms-ms_observations.R	Tue Dec 18 09:50:50 2018 -0500
@@ -0,0 +1,106 @@
+# 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)
+  }
+}
+
+nb_obs_PeptideAtlas <- function(input, atlas_file) {
+  ## Calculate the sum of n_observations for each ID in input
+  atlas = read_file(atlas_file, T)
+  return(atlas$nb_obs[match(input,atlas$Uniprot_AC)])
+}
+
+main = function() {
+  args <- commandArgs(TRUE)
+  if(length(args)<1) {
+    args <- c("--help")
+  }
+  
+  # Help section
+  if("--help" %in% args) {
+    cat("Selection and Annotation HPA
+    Arguments:
+        --input_type: type of input (list of id or filename)
+        --input: input
+        --atlas: list of file(s) path to use
+        --output: text 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/retrieve_msbased_pepatlas/args.Rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/retrieve_msbased_pepatlas/args.Rda")
+  
+  # Extract input
+  input_type = args$input_type
+  if (input_type == "list") {
+    input = strsplit(args$input, "[ \t\n]+")[[1]]
+  } else if (input_type == "file") {
+    filename = args$input
+    ncol = args$column
+    # Check ncol
+    if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
+      stop("Please enter an integer for level")
+    } else {
+      ncol = as.numeric(gsub("c", "", ncol))
+    }
+    header = str2bool(args$header)
+    file = read_file(filename, header)
+    input = sapply(file[,ncol],function(x) strsplit(as.character(x),";")[[1]][1],USE.NAMES = F)
+  }
+
+  output = args$output
+
+  #function to create a list of infos from file path
+  extract_info_from_path <- function(path) {
+    file_name=strsplit(tail(strsplit(path,"/")[[1]],n=1),"\\.")[[1]][1]
+    date=tail(strsplit(file_name,"_")[[1]],n=1)
+    tissue=paste(strsplit(file_name,"_")[[1]][1:2],collapse="_")
+    return (c(date,tissue,file_name,path))
+  }
+  
+  #data_frame building
+  paths=strsplit(args$atlas,",")[[1]]
+  tmp <- sapply(paths, extract_info_from_path,USE.NAMES = FALSE)
+  df <- as.data.frame(t(as.data.frame(tmp)),row.names = c(""),stringsAsFactors = FALSE)
+  names(df) <- c("date","tissue","filename","path")
+  
+  # Annotations
+  res = sapply(df$path, function(x) nb_obs_PeptideAtlas(input, x), USE.NAMES = FALSE)
+  
+  colnames(res)=df$filename
+
+  # Write output
+  if (input_type == "list") {
+    res = cbind(as.matrix(input), res)
+    colnames(res)[1] = "Uniprot accession number"
+  } else if (input_type == "file") {
+    res = cbind(file, res)
+  }
+  res = as.data.frame(apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x)))
+  write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE)
+  
+}
+
+main()
+#Rscript retrieve_peptideatlas.R --input_type="file" --input="test-data/FKW_Lacombe_et_al_2017_OK.txt" --atlas_brain="Human_Brain_201803_PeptideAtlas.txt" --column="c1" --header="true"  --output="test-data/PeptideAtlas_output.txt"  --atlas_urine="Human_Urine_201803_PeptideAtlas.txt" --atlas="brain,urine"
+