comparison get_data_HPA_v2.R @ 5:f15cdeeba4b4 draft

planemo upload commit 4af7ac25de19ca10b1654820e909c647a2d337b2-dirty

4:2f95774977ff

#	--column : column containing in input ENSG identifiers
#	--select : information from HPA to select, may be
#	: RNA.tissue.category,Reliability..IH.,Reliability..IF. (comma-separated)
# --output : output file name
# Useful functions

'%!in%' <- function(x,y)!('%in%'(x,y))

args = commandArgs(trailingOnly = TRUE)

  sample = sample[,column]
}
if (typeinput=="tabfile"){
  
  if (header=="TRUE"){
    listfile = read.table(listfile,header=TRUE,sep="\t",quote="\"",fill=TRUE, na.strings=c("","NA"))
  }else{
    listfile = read.table(listfile,header=FALSE,sep="\t",quote="\"",fill=TRUE, na.strings=c("","NA"))
  }
  sample = listfile[,column]

}

  data = data[,to_keep]
  # if only some of the proteins were not found in proteinatlas they will be added to
  # the file with the fields "Protein not found in proteinatlas"
  if (length(which(sample %!in% proteinatlas[,3]))!=0){
    proteins_not_found = as.data.frame(sample[which(sample %!in% proteinatlas[,3])])
	proteins_not_found = cbind(proteins_not_found,matrix(rep("Protein not found in HPA",length(proteins_not_found)),nrow=length(proteins_not_found),ncol=length(colnames(data))-1))

    colnames(proteins_not_found)=colnames(data) 
	
    data = rbind(data,proteins_not_found)
  }

5:f15cdeeba4b4

#	--column : column containing in input ENSG identifiers
#	--select : information from HPA to select, may be
#	: RNA.tissue.category,Reliability..IH.,Reliability..IF. (comma-separated)
# --output : output file name
# Useful functions

# 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 = "")
    #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 = "")
    # Remove empty rows
    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
    #And assign the header to the data
    names(file) <- headers
  }
  else {
    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
    # Remove empty rows
    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
  }
  return(file)
}

'%!in%' <- function(x,y)!('%in%'(x,y))

args = commandArgs(trailingOnly = TRUE)

  sample = sample[,column]
}
if (typeinput=="tabfile"){
  
  if (header=="TRUE"){
    listfile = readfile(listfile, "true")
  }else{
    listfile = readfile(listfile, "false")
  }
  sample = listfile[,column]

}

  data = data[,to_keep]
  # if only some of the proteins were not found in proteinatlas they will be added to
  # the file with the fields "Protein not found in proteinatlas"
  if (length(which(sample %!in% proteinatlas[,3]))!=0){
    proteins_not_found = as.data.frame(sample[which(sample %!in% proteinatlas[,3])])
	  proteins_not_found = cbind(proteins_not_found,matrix(rep("Protein not found in HPA",length(proteins_not_found)),nrow=length(proteins_not_found),ncol=length(colnames(data))-1))

    colnames(proteins_not_found)=colnames(data) 
	
    data = rbind(data,proteins_not_found)
  }