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Merge pull request #8 from omixer/7-missing-file
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‎.gitignore

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.bash_history
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.idea
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.project
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.settings
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.RData

‎DESCRIPTION

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Package: omixerRpm
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Type: Package
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Title: Metabolic module profiling of microbiome samples
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Version: 0.3.2
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Date: 2018-11-13
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Version: 0.3.3
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Date: 2022-12-16
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Author: Youssef Darzi
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Maintainer: Youssef Darzi<youssef.darzi@gmail.com>
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Maintainer: Youssef Darzi<youssef.darzi@omixer.io>
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Description: An R interface to the omixer-rpm for metabolic module profiling of microbiome samples
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License: GNU General Public License v3.0. The bundled omixer-rpm.jar is licensed under an Academic Non-commercial Software License Agreement, https://github.com/raeslab/omixer-rpm/blob/master/LICENSE

‎R/rpm.R

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# x is a dataframe or a valid file path
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# Add the Description of modules as a data object
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rpm <- function(x, minimum.coverage=-1, score.estimator="median", annotation = 1, module.db = NULL, threads = 1,
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normalize.by.length = FALSE, distribute = FALSE, java.mem=NULL) {
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# link to the GMMs executable and DB
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rpm.exec <- system.file("java", "omixer-rpm.jar", package = "omixerRpm")
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if(is.null(module.db)) {
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module.db <- loadDefaultDB()
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}
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# Prepare output directories
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out.dir <- tempfile()
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dir.create(out.dir)
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# Is x a file or a data.frame
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if(!is.character(x)) {
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# write samples for processing with the GMMs
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in.dir <- tempfile()
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dir.create(in.dir)
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input <- file.path(in.dir, "input.tsv")
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write.table(x, input, col.names=T, row.names=F, quote=F, sep="\t")
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} else {
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input <- x
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}
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rpm <- function(x, minimum.coverage = -1, score.estimator = "median", annotation = 1, module.db = NULL, threads = 1,
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normalize.by.length = FALSE, distribute = FALSE, java.mem = NULL) {
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# link to the GMMs executable and DB
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rpm.exec <- system.file("java", "omixer-rpm.jar", package = "omixerRpm")
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if (is.null(module.db)) {
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module.db <- loadDefaultDB()
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}
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# Compiling the command
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command <- "java -server"
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if(!is.null(java.mem)){
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command <- paste(command, paste0("-Xmx", java.mem, "G"))
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}
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command <- paste(command , "-jar", rpm.exec,
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"-c" , minimum.coverage,
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"-s", score.estimator,
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"-d", file.path(module.db@directory, module.db@modules),
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"-i", input,
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"-o", out.dir,
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"-a", annotation,
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"-t", threads,
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"-e", 2)
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if( normalize.by.length == TRUE) {
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command <-paste(command, "-n")
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}
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if( distribute == TRUE) {
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command <-paste(command, "--Xdistribute")
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}
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# Run the module mapping
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tryCatch({
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system(command)
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},
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warning = function (e) {
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print(e)
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if(e$message == "error in running command"){
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stop(e)
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}
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},
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error = function (e) {
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print(geterrmessage())
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stop(e)
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}
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)
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# Prepare output directories
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out.dir <- tempfile()
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dir.create(out.dir)
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abundance <- read.table(file.path(out.dir, "modules.tsv"), sep="\t", header=TRUE)
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coverage <- read.table(file.path(out.dir, "modules-coverage.tsv"), sep="\t", header=TRUE)
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annotation.df <- NULL
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if (annotation == 1){
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# ortohology only
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abundance.colnames <- colnames(abundance)
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annotation.df <- as.data.frame(abundance[, 1])
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abundance <- as.data.frame(abundance[, -c(1)])
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coverage <- as.data.frame(coverage[, -c(1)])
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colnames(annotation.df) <- abundance.colnames[1]
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colnames(abundance) <- abundance.colnames[2:length(abundance.colnames)]
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colnames(coverage) <- abundance.colnames[2:length(abundance.colnames)]
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} else if (annotation == 2) {
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# orthology and taxonomy
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abundance.colnames <- colnames(abundance)
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annotation.df <- as.data.frame(abundance[, c(1, 2)])
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abundance <- as.data.frame(abundance[, -c(1, 2)])
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coverage <- as.data.frame(coverage[, -c(1, 2)])
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colnames(annotation.df) <- abundance.colnames[1:2]
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colnames(abundance) <- abundance.colnames[3:length(abundance.colnames)]
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colnames(coverage) <- abundance.colnames[3:length(abundance.colnames)]
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}
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Modules(abundance=abundance, coverage=coverage, annotation=annotation.df, db=module.db)
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# Is x a file or a data.frame
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if (!is.character(x)) {
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# write samples for processing with the GMMs
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in.dir <- tempfile()
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dir.create(in.dir)
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input <- file.path(in.dir, "input.tsv")
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write.table(x, input, col.names = T, row.names = F, quote = F, sep = "\t")
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} else {
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input <- x
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}
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# Compiling the command
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command <- "java -server"
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29+
if (!is.null(java.mem)) {
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command <- paste(command, paste0("-Xmx", java.mem, "G"))
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}
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command <- paste(command, "-jar", rpm.exec,
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"-c", minimum.coverage,
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"-s", score.estimator,
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"-d", file.path(module.db@directory, module.db@modules),
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"-i", input,
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"-o", out.dir,
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"-a", annotation,
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"-t", threads,
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"-e", 2)
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if (normalize.by.length == TRUE) {
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command <- paste(command, "-n")
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}
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if (distribute == TRUE) {
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command <- paste(command, "--Xdistribute")
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}
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# Run the module mapping
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tryCatch({
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status <- system(command)
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if (status != 0) {
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stop("The execution of Omixer-RPM returned a non-zero exit status. Refer to the exception output for details.")
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}
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},
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warning = function(e) {
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print(e)
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if (e$message == "error in running command") {
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stop(e)
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}
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},
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error = function(e) {
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print(geterrmessage())
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stop(e)
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}
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)
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abundance <- read.table(file.path(out.dir, "modules.tsv"), sep = "\t", header = TRUE)
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coverage <- read.table(file.path(out.dir, "modules-coverage.tsv"), sep = "\t", header = TRUE)
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annotation.df <- NULL
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74+
if (annotation == 1) {
75+
# ortohology only
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abundance.colnames <- colnames(abundance)
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annotation.df <- as.data.frame(abundance[, 1])
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abundance <- as.data.frame(abundance[, -c(1)])
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coverage <- as.data.frame(coverage[, -c(1)])
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colnames(annotation.df) <- abundance.colnames[1]
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colnames(abundance) <- abundance.colnames[2:length(abundance.colnames)]
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colnames(coverage) <- abundance.colnames[2:length(abundance.colnames)]
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} else if (annotation == 2) {
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# orthology and taxonomy
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abundance.colnames <- colnames(abundance)
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annotation.df <- as.data.frame(abundance[, c(1, 2)])
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abundance <- as.data.frame(abundance[, -c(1, 2)])
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coverage <- as.data.frame(coverage[, -c(1, 2)])
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colnames(annotation.df) <- abundance.colnames[1:2]
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colnames(abundance) <- abundance.colnames[3:length(abundance.colnames)]
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colnames(coverage) <- abundance.colnames[3:length(abundance.colnames)]
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}
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Modules(abundance = abundance, coverage = coverage, annotation = annotation.df, db = module.db)
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}

‎test/runitModules.R

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@@ -67,4 +67,9 @@ test.moduleDbLoad <- function() {
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db <- loadDB("GMMs.v1.07")
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# check getNames returns the correct annotation
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checkEquals(getNames(db, "MF0010"), "sucrose degradation I")
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}
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}
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test.handleMalformedInput <- function() {
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# expect a NumberFormat exception for the wrong annotation value
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checkException(rpm("test/species_matrix.tsv", annotation = 1, minimum.coverage = 0.3))
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}

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