Mercurial > repos > proteore > proteore_expression_levels_by_tissue
view get_expression_profiles.R @ 10:48b767deb90b draft
planemo upload commit b052261cf5cd6c2413e301a19d5c95d9794f1e81-dirty
author | proteore |
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date | Wed, 13 Mar 2019 09:23:41 -0400 |
parents | 2c0bab71a436 |
children | 56c93d1fc8fd |
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# Read file and return file content as data.frame read_file <- function(path,header){ file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE) if (inherits(file,"try-error")){ stop("File not found !") }else{ return(file) } } 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) } } # input has to be a list of IDs in ENSG format # tissue is one of unique(HPA.normal.tissue$Tissue) # level is one, or several, or 0 (=ALL) of "Not detected", "Medium", "High", "Low" # reliability is one, or several, or 0 (=ALL) of "Approved", "Supported", "Uncertain" annot.HPAnorm<-function(input, HPA_normal_tissue, tissue, level, reliability, not_mapped_option) { dat <- subset(HPA_normal_tissue, Gene %in% input) res.Tissue<-subset(dat, Tissue %in% tissue) res.Level<-subset(res.Tissue, Level %in% level) res.Rel<-subset(res.Level, Reliability %in% reliability) if (not_mapped_option) { if (length(setdiff(intersect(input, unique(dat$Gene)), unique(res.Rel$Gene)))>0) { not_match_IDs <- matrix(setdiff(intersect(input, unique(dat$Gene)), unique(res.Rel$Gene)), ncol = 1, nrow = length(setdiff(intersect(input, unique(dat$Gene)), unique(res.Rel$Gene)))) not.match <- matrix("no match", ncol = ncol(HPA_normal_tissue) - 1, nrow = length(not_match_IDs)) not.match <- cbind(not_match_IDs, unname(not.match)) colnames(not.match) <- colnames(HPA_normal_tissue) res <- rbind(res.Rel, not.match) } else { res <- res.Rel } if (length(setdiff(input, unique(dat$Gene)))>0) { not.mapped <- matrix(ncol = ncol(HPA_normal_tissue) - 1, nrow = length(setdiff(input, unique(dat$Gene)))) not.mapped <- cbind(matrix(setdiff(input, unique(dat$Gene)), ncol = 1, nrow = length(setdiff(input, unique(dat$Gene)))), unname(not.mapped)) colnames(not.mapped) <- colnames(HPA_normal_tissue) res <- rbind(res, not.mapped) } } else { res <- res.Rel } return(res) } annot.HPAcancer<-function(input, HPA_cancer_tissue, cancer, not_mapped_option) { dat <- subset(HPA_cancer_tissue, Gene %in% input) res.Cancer<-subset(dat, Cancer %in% cancer) if (not_mapped_option) { not.mapped <- matrix(ncol=ncol(HPA_cancer_tissue)-1, nrow=length(setdiff(input, unique(dat$Gene)))) not.mapped <- cbind(matrix(setdiff(input, unique(dat$Gene)), ncol = 1, nrow = length(setdiff(input, unique(dat$Gene)))), unname(not.mapped)) colnames(not.mapped) <- colnames(HPA_cancer_tissue) res <- rbind(res.Cancer, not.mapped) } else { res <- res.Cancer } return(res) } main <- function() { args <- commandArgs(TRUE) if(length(args)<1) { args <- c("--help") } # Help section if("--help" %in% args) { cat("Selection and Annotation HPA Arguments: --ref_file: HPA normal/cancer tissue file path --input_type: type of input (list of id or filename) --input: list of IDs in ENSG format --column_number: the column number which you would like to apply... --header: true/false if your file contains a header --atlas: normal/cancer if normal: --tissue: list of tissues --level: Not detected, Low, Medium, High --reliability: Supportive, Uncertain if cancer: --cancer: Cancer tissues --not_mapped: true/false if your output file should contain not-mapped and not-match IDs --output: output filename \n") q(save="no") } # Parse arguments 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 #save(args,file = "/home/dchristiany/proteore_project/ProteoRE/tools/Get_expression_profiles/args.rda") #load("/home/dchristiany/proteore_project/ProteoRE/tools/Get_expression_profiles/args.rda") # Extract input input_type = args$input_type if (input_type == "list") { list_id = strsplit(args$input, "[ \t\n]+")[[1]] } else if (input_type == "file") { filename = args$input column_number = as.numeric(gsub("c", "" ,args$column_number)) header = str2bool(args$header) file = read_file(filename, header) list_id = sapply(strsplit(file[,column_number], ";"), "[", 1) } input = list_id # Read reference file reference_file = read_file(args$ref_file, TRUE) # Extract other options atlas = args$atlas not_mapped_option = str2bool(args$not_mapped) if (atlas=="normal") { tissue = strsplit(args$tissue, ",")[[1]] level = strsplit(args$level, ",")[[1]] reliability = strsplit(args$reliability, ",")[[1]] # Calculation res = annot.HPAnorm(input, reference_file, tissue, level, reliability, not_mapped_option) } else if (atlas=="cancer") { cancer = strsplit(args$cancer, ",")[[1]] # Calculation res = annot.HPAcancer(input, reference_file, cancer, not_mapped_option) } # Write output output = args$output res <- apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x)) write.table(res, output, sep = "\t", quote = FALSE, row.names = FALSE) } main()