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Switch to alserglab.wustl.edu/hsds, support for ARCHS4 v2.3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,18 @@ | ||
| Package: phantasusLite | ||
| Type: Package | ||
| Title: Loading and annotation RNA-Seq counts matrices | ||
| Version: 1.1.0 | ||
| Title: Loading and annotation RNA-seq counts matrices | ||
| Version: 1.1.1 | ||
| Authors@R: c(person("Rita", "Sablina", role = "aut"), | ||
| person("Maxim", "Kleverov", role = "aut"), | ||
| person("Alexey", "Sergushichev", email = "[email protected]", role = c("aut", "cre"))) | ||
| Description: PhantasusLite – a lightweight package with helper functions of general interest | ||
| extracted from phantasus package. In parituclar it simplifies working with public | ||
| RNA-seq datasets from GEO by providing access to the remote | ||
| HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects. | ||
| Depends: R (>= 4.3) | ||
| Depends: R (>= 4.2) | ||
| Imports: | ||
| data.table, | ||
| rhdf5client(>= 1.21.5), | ||
| rhdf5client(>= 1.25.1), | ||
| httr, stringr, | ||
| stats, | ||
| utils, | ||
|
|
@@ -22,7 +22,7 @@ biocViews: GeneExpression, Transcriptomics, RNASeq | |
| License: MIT + file LICENSE | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 7.2.3 | ||
| RoxygenNote: 7.3.1 | ||
| Suggests: | ||
| testthat (>= 3.0.0), | ||
| knitr, | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| Changes in version 1.2.0 | ||
| * Switch to https://alserglab.wustl.edu/hsds remote for default HSDS server | ||
| * Depending on rhdf5client >= 1.25.1 to support ARCHS4 v2.3 files |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,48 +1,48 @@ | ||
| #' Returns list of all HDF5-files on HSDS-server | ||
| #' @param url, containing url of the server and root domain. | ||
| #' @param directory, containing name of the directory | ||
| #' | ||
| #' @return List of all HDF5-files on the server or all files of the collection | ||
| #' | ||
| #' @export | ||
| #' @import rhdf5client | ||
| #' @examples | ||
| #' url <- 'https://ctlab.itmo.ru/hsds/?domain=/counts' | ||
| #' getHSDSFileList(url) | ||
| #' | ||
|
|
||
| getHSDSFileList <- function(url='https://ctlab.itmo.ru/hsds/?domain=/counts', directory = NULL) { | ||
| src <- httr::parse_url(url) | ||
| dir <- src$query$domain | ||
| src <- paste0(src$scheme,'://',src$hostname,'/',src$path) | ||
| src <- HSDSSource(src) | ||
| hdf5FileList <- list() | ||
| if (is.null(directory)) { | ||
| directories <- listDomains(src, dir) | ||
| directories <- directories[-grep("*\\.h5$", directories)] | ||
| directories <- gsub(paste0(dir, '/'), '', directories) | ||
| for (directory in directories) { | ||
| request <- paste0(src@endpoint, "/domains?domain=", | ||
| dir, '/', directory) | ||
| response <- rhdf5client:::submitRequest(request) | ||
| domains <- response[["domains"]] | ||
| for (domain in domains) { | ||
| if (domain$name != paste0(dir, "/", directory, '/', directory, ".h5")) { | ||
| hdf5FileList <- append(hdf5FileList, domain$name) | ||
| } | ||
| } | ||
| } | ||
| } else { | ||
| request <- paste0(src@endpoint, "/domains?domain=", | ||
| dir, '/', directory) | ||
| response <- rhdf5client:::submitRequest(request) | ||
| domains <- response[["domains"]] | ||
| for (domain in domains) { | ||
| if (domain$name != paste0(dir, "/", directory, '/', directory, ".h5")) { | ||
| hdf5FileList <- append(hdf5FileList, domain$name) | ||
| } | ||
| } | ||
| } | ||
| hdf5FileList <- unlist(hdf5FileList) | ||
| return(hdf5FileList) | ||
| } | ||
| #' Returns list of all HDF5-files on HSDS-server | ||
| #' @param url, containing url of the server and root domain. | ||
| #' @param directory, containing name of the directory | ||
| #' | ||
| #' @return List of all HDF5-files on the server or all files of the collection | ||
| #' | ||
| #' @export | ||
| #' @import rhdf5client | ||
| #' @examples | ||
| #' url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' | ||
| #' getHSDSFileList(url) | ||
| #' | ||
|
|
||
| getHSDSFileList <- function(url='https://alserglab.wustl.edu/hsds/?domain=/counts', directory = NULL) { | ||
| src <- httr::parse_url(url) | ||
| dir <- src$query$domain | ||
| src <- paste0(src$scheme,'://',src$hostname,'/',src$path) | ||
| src <- HSDSSource(src) | ||
| hdf5FileList <- list() | ||
| if (is.null(directory)) { | ||
| directories <- listDomains(src, dir) | ||
| directories <- directories[-grep("*\\.h5$", directories)] | ||
| directories <- gsub(paste0(dir, '/'), '', directories) | ||
| for (directory in directories) { | ||
| request <- paste0(src@endpoint, "/domains?domain=", | ||
| dir, '/', directory) | ||
| response <- rhdf5client:::submitRequest(request) | ||
| domains <- response[["domains"]] | ||
| for (domain in domains) { | ||
| if (domain$name != paste0(dir, "/", directory, '/', directory, ".h5")) { | ||
| hdf5FileList <- append(hdf5FileList, domain$name) | ||
| } | ||
| } | ||
| } | ||
| } else { | ||
| request <- paste0(src@endpoint, "/domains?domain=", | ||
| dir, '/', directory) | ||
| response <- rhdf5client:::submitRequest(request) | ||
| domains <- response[["domains"]] | ||
| for (domain in domains) { | ||
| if (domain$name != paste0(dir, "/", directory, '/', directory, ".h5")) { | ||
| hdf5FileList <- append(hdf5FileList, domain$name) | ||
| } | ||
| } | ||
| } | ||
| hdf5FileList <- unlist(hdf5FileList) | ||
| return(hdf5FileList) | ||
| } |
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