Mercurial > repos > proteore > proteore_prot_features
view get_data_nextprot.R @ 0:e3b52db3d583 draft
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
author | proteore |
---|---|
date | Sun, 26 Nov 2017 19:45:52 -0500 |
parents | |
children |
line wrap: on
line source
# 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) }