--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data_nextprot.R	Sun Nov 26 19:45:52 2017 -0500
@@ -0,0 +1,138 @@
+# Usage : Rscript --vanilla get_data_nextprot.R --inputtype copypaste (or
+# tabfile) --input file.txt --nextprot result_nextprot.txt --column column
+# --argsP1 IsoPoint,SeqLength,MW
+# --argsP2 Chr,SubcellLocations --argsP3 Diseases --type id nextprot (uniprot)
+# --output output.txt --header TRUE
+
+# e.g : 
+# Rscript --vanilla get_data_nextprot.R --inputtype copypaste  --input P01133 P00533 P62158 Q16566 P31323 P17612 P10644
+# P22612 P31321 P13861 P22694 P25098 P16220 Q14573 Q14571 Q14643 Q05655 Q02156
+# P19174 O43865 Q01064 P54750 Q14123 P51828 Q08828 O60266 Q08462 O60503 O43306
+# Q8NFM4 O95622 P40145 P17252 P05129 --nextprot
+# result_nextprot.txt--column c1 --argsP1 IsoPoint --argsP2
+# Chr --argsP3 Diseases --typeid uniprot --output output.txt --header FALSE
+
+# Useful functions
+
+'%!in%' <- function(x,y)!('%in%'(x,y))
+
+# Parse arguments
+
+args = commandArgs(trailingOnly = TRUE)
+
+# create a list of the arguments from the command line, separated by a blank space
+hh <- paste(unlist(args),collapse=' ')
+# delete the first element of the list which is always a blank space
+listoptions <- unlist(strsplit(hh,'--'))[-1]
+# for each input, split the arguments with blank space as separator, unlist, and delete the first element which is the input name (e.g --protalas) 
+options.args <- sapply(listoptions,function(x){
+         unlist(strsplit(x, ' '))[-1]
+        })
+# same as the step above, except that only the names are kept
+options.names <- sapply(listoptions,function(x){
+  option <-  unlist(strsplit(x, ' '))[1]
+})
+names(options.args) <- unlist(options.names)
+
+
+typeinput = as.character(options.args[1])
+nextprot = read.table(as.character(options.args[3]),header=TRUE,sep="\t",quote="\"") 
+listfile = as.character(options.args[2])
+column = as.numeric(gsub("c","",options.args[4]))
+P1_args = as.character(options.args[5])
+P2_args = as.character(options.args[6])
+P3_args = as.character(options.args[7])
+typeid = as.character(options.args[8])
+filename = as.character(options.args[9])
+header = as.character(options.args[10])
+
+if (typeinput=="copypaste"){
+  sample = as.data.frame(unlist(listfile))
+  sample = sample[,column]
+}
+if (typeinput=="tabfile"){
+  
+  if (header=="TRUE"){
+    listfile = read.table(listfile,header=TRUE,sep="\t",quote="\"",fill=TRUE)
+  }else{
+    listfile = read.table(listfile,header=FALSE,sep="\t",quote="\"",fill=TRUE)
+  }
+  sample = listfile[,column]
+
+}
+# Change the sample ids if they are uniprot ids to be able to match them with
+# Nextprot data
+if (typeid=="uniprot"){
+  sample = gsub("^","NX_",sample)
+}
+
+# Select user input protein ids in nextprot
+
+if ((length(sample[sample %in% nextprot[,1]]))==0){
+
+    write.table("None of the input ids are can be found in Nextprot",file=filename,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
+
+}else{ 
+
+	
+	to_keep = c()
+	
+	if (P1_args!="None"){
+	  P1_args = unlist(strsplit(P1_args,","))
+	  for (arg in P1_args){
+	    colnb = which(colnames(nextprot) %in% c(arg))
+	    to_keep = c(to_keep,colnb)    
+	  }
+	}
+	
+	if (P2_args!="None"){
+	  P2_args = unlist(strsplit(P2_args,","))
+	  for (arg in P2_args){
+	    colnb = which(colnames(nextprot) %in% c(arg))
+	    to_keep = c(to_keep,colnb)    
+	  }
+	}
+	
+	if (P3_args!="None"){
+	  P3_args = unlist(strsplit(P3_args,","))
+	  for (arg in P3_args){
+	    colnb = which(colnames(nextprot) %in% c(arg))
+	    to_keep = c(to_keep,colnb)    
+	  }
+	}
+	to_keep = c(1,to_keep)
+	lines = which(nextprot[,1] %in% sample)
+  data = nextprot[lines,]
+  
+  data = data[,to_keep]
+
+
+  # if only some of the proteins were not found in nextprot they will be added to
+	# the file with the fields "Protein not found in Nextprot"
+	if (length(which(sample %!in% nextprot[,1]))!=0){
+	  proteins_not_found = as.data.frame(sample[which(sample %!in% nextprot[,1])])
+	
+	  proteins_not_found = cbind(proteins_not_found,matrix(rep("Protein not found in Nextprot",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)
+	}
+  
+  # Merge original data and data selected from nextprot
+
+  # Before that, if the initial ids were uniprot ids change them back from
+  # Nextprot to uniprot ids in data 
+  if (typeid=="uniprot"){
+    data[,1] = gsub("^NX_","",data[,1])
+  }
+  data = merge(listfile, data, by.x = column, by.y=1)
+  if (typeid=="uniprot"){
+    colnames(data)[1] = "UniprotID"	
+  }
+  if (typeid=="nextprot"){
+    colnames(data)[1] = "NextprotID"	
+  }
+  # Write result
+  write.table(data,file=filename,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
+	
+}