Mercurial > repos > proteore > proteore_prot_features
diff add_protein_features.R @ 9:0b46a7aead62 draft
planemo upload commit eb7450f36863f02f036cbc52bf5525d68f22bd9e
author | proteore |
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date | Tue, 18 Dec 2018 08:26:55 -0500 |
parents | |
children | 8df559ad14a7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/add_protein_features.R Tue Dec 18 08:26:55 2018 -0500 @@ -0,0 +1,202 @@ +# Read file and return file content as data.frame +read_file <- function(path,header){ + file <- try(read.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="", check.names = F),silent=TRUE) + if (inherits(file,"try-error")){ + stop("File not found !") + }else{ + file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE] + return(file) + } +} + +order_columns <- function (df,ncol,id_type,file){ + if (id_type=="Uniprot_AC"){ncol=ncol(file)} + if (ncol==1){ #already at the right position + return (df) + } else { + df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])] + } + return (df) +} + +get_list_from_cp <-function(list){ + list = strsplit(list, "[ \t\n]+")[[1]] + list = gsub("NA","",list) + list = list[list != ""] #remove empty entry + list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2") + return(list) +} + +get_args <- function(){ + + ## Collect arguments + args <- commandArgs(TRUE) + + ## Default setting when no arguments passed + if(length(args) < 1) { + args <- c("--help") + } + + ## Help section + if("--help" %in% args) { + cat("Selection and Annotation HPA + Arguments: + --inputtype: type of input (list of id or filename) + --input: input + --nextprot: path to nextprot information file + --column: the column number which you would like to apply... + --header: true/false if your file contains a header + --type: the type of input IDs (Uniprot_AC/EntrezID) + --pc_features: IsoPoint,SeqLength,MW + --localization: Chr,SubcellLocations + --diseases_info: Diseases + --output: text output filename \n") + + q(save="no") + } + + 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 + + return(args) +} + +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) + } +} + +#take data frame, return data frame +split_ids_per_line <- function(line,ncol){ + + #print (line) + header = colnames(line) + line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol]) + + if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) { + if (length(line)==1 ) { + lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F) + } else { + if (ncol==1) { #first column + lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)])) + } else if (ncol==length(line)) { #last column + lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";")))) + } else { + lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)])) + } + } + colnames(lines)=header + return(lines) + } else { + return(line) + } +} + +#create new lines if there's more than one id per cell in the columns in order to have only one id per line +one_id_one_line <-function(tab,ncol){ + + if (ncol(tab)>1){ + + tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x)) + header=colnames(tab) + res=as.data.frame(matrix(ncol=ncol(tab),nrow=0)) + for (i in 1:nrow(tab) ) { + lines = split_ids_per_line(tab[i,],ncol) + res = rbind(res,lines) + } + }else { + res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F) + res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F) + colnames(res)=colnames(tab) + } + return(res) +} + +# Get information from neXtProt +get_nextprot_info <- function(nextprot,input,pc_features,localization,diseases_info){ + if(diseases_info){ + cols = c("NextprotID",pc_features,localization,"Diseases") + } else { + cols = c("NextprotID",pc_features,localization) + } + + cols=cols[cols!="None"] + info = nextprot[match(input,nextprot$NextprotID),cols] + return(info) +} + +protein_features = function() { + + args <- get_args() + + #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda") + #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda") + + #setting variables + inputtype = args$inputtype + if (inputtype == "copy_paste") { + input = get_list_from_cp(args$input) + file = data.frame(input,stringsAsFactors = F) + ncol=1 + } else if (inputtype == "file") { + filename = args$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) # Get file content + if (any(grep(";",file[,ncol]))) {file = one_id_one_line(file,ncol)} + if (args$type == "NextprotID" && ! "NextprotID" %in% colnames(file)) { colnames(file)[ncol] <- "NextprotID" + } else if (args$type == "NextprotID" && "NextprotID" %in% colnames(file) && match("NextprotID",colnames(file))!=ncol ) { + colnames(file)[match("NextprotID",colnames(file))] <- "old_NextprotID" + colnames(file)[ncol] = "NextprotID" + } + } + + # Read reference file + nextprot = read_file(args$nextprot,T) + + # Parse arguments + id_type = args$type + pc_features = strsplit(args$pc_features, ",")[[1]] + localization = strsplit(args$localization, ",")[[1]] + diseases_info = str2bool(args$diseases_info) + output = args$output + + # Change the sample ids if they are Uniprot_AC ids to be able to match them with + # Nextprot data + if (id_type=="Uniprot_AC"){ + NextprotID = gsub("^NX_$","",gsub("^","NX_",file[,ncol])) + file = cbind(file,NextprotID) + if (inputtype=="copy_paste") {colnames(file)[1]="Uniprot-AC"} + ncol=ncol(file) + } + NextprotID = file[,ncol] + + #Select user input protein ids in nextprot + #NextprotID = unique(NextprotID[which(!is.na(NextprotID[NextprotID!=""]))]) + if (all(!NextprotID %in% nextprot[,1])){ + write.table("None of the input ids can be found in Nextprot",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE) + } else { + res <- get_nextprot_info(nextprot,NextprotID,pc_features,localization,diseases_info) + res = res[!duplicated(res$NextprotID),] + output_content = merge(file, res,by.x=ncol,by.y="NextprotID",incomparables = NA,all.x=T) + output_content = order_columns(output_content,ncol,id_type,file) + output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA + write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE) + } + +} +protein_features()