# HG changeset patch # User proteore # Date 1511743552 18000 # Node ID e3b52db3d5836b33878a6398d247cdfeec93fe9c planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty diff -r 000000000000 -r e3b52db3d583 get_data_nextprot.R --- /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) + +} diff -r 000000000000 -r e3b52db3d583 prot_features.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prot_features.xml Sun Nov 26 19:45:52 2017 -0500 @@ -0,0 +1,145 @@ + + +obtains different features of your protein list from neXtProt. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+ + + + + + + + + + +