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getENSEMBLInfo.R
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getENSEMBLInfo.R
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#' @title Retrieve ENSEMBL info file
#' @description Retrieve species and genome information from
#' http://rest.ensembl.org/info/species?content-type=application/json/.
#' @param update logical, default FALSE. If TRUE, update cached list,
#' if FALSE use existing cache (if it exists). For cache location see
#' \code{cachedir()}
#' @param divisions character, name of divisions to check, default is all from
#' \code{ensembl_divisions()}. If NULL, also all is used.
#' @author Hajk-Georg Drost
#' @return a tibble table storing info for all available ENSEMBL divisions.
#' @examples
#' \dontrun{
#' # look at available divisions
#' ensembl_divisions()
#' # retrieve information for all ENSEMBL divisions at once
#' test <- getENSEMBLInfo()
#' test
#' # retrieve information for a particular ENSEMBL division (e.g. EnsemblVertebrates)
#' test_vertebrates <- get.ensembl.info(update = TRUE, division = "EnsemblVertebrates")
#' test_vertebrates
#' }
#' @seealso \code{\link{ensembl_divisions}}, \code{\link{get.ensembl.info}}, \code{\link{getKingdomAssemblySummary}}
#' @export
getENSEMBLInfo <- function(update = FALSE, divisions = ensembl_divisions()) {
all_divisions <- ensembl_divisions()
if (is.null(divisions)) divisions <- all_divisions
if (!all(divisions %in% all_divisions))
stop("Specified Ensembl divisions must be subset of:\n",
paste(all_divisions, collapse = " "))
ENSEMBLInfoTable <- vector("list", length(divisions))
for (i in seq_len(length(divisions))) {
cat("Starting information retrieval for:", divisions[i])
cat("\n")
ENSEMBLInfoTable[[i]] <-
get.ensembl.info(update, division = divisions[i])
}
return(dplyr::bind_rows(ENSEMBLInfoTable))
}
ensembl_assembly_hits <- function(organism) {
ensembl_summary <-
suppressMessages(is.genome.available.ensembl(
organism = organism,
db = "ensembl",
details = TRUE
))
if (nrow(ensembl_summary) == 0) {
message(
"Unfortunately, organism '",
organism,
"' does not exist in this database. ",
"Could it be that the organism name is misspelled? Thus, download has been omitted."
)
return(FALSE)
}
ensembl_summary <-
ensembl_summaries_filter(ensembl_summary, organism)
return(ensembl_summary)
}
ensembl_summaries_filter <- function(ensembl_summary, organism) {
if (nrow(ensembl_summary) > 1) {
taxon_id <- assembly <- name <- accession <- NULL
ensembl_summary_copy <- ensembl_summary
if (is.taxid(organism)) {
ensembl_summary <-
dplyr::filter(ensembl_summary,
taxon_id == as.integer(organism),
!is.na(assembly))
} else {
ensembl_summary <-
dplyr::filter(
ensembl_summary,
(name == lower_cap_underscore_organism_name(organism)) |
(accession == organism),
!is.na(assembly)
)
if (nrow(ensembl_summary) == 0) {
ensembl_summary <-
dplyr::filter(ensembl_summary_copy, !is.na(assembly))
}
}
if (nrow(ensembl_summary) == 0) {
print(ensembl_summary_copy)
stop("All assemblies removed by filter (more info in lines above)")
}
}
return(ensembl_summary)
}
is.taxid <- function(x) {
return(stringr::str_count(x, "[:digit:]") == nchar(x))
}
validate_release <- function(release, ensembl_summary) {
if (!is.null(release)) {
release <- as.numeric(release)
if (!is.element(release, ensembl_all_releases()))
stop("Please provide a release number that is supported by ENSEMBL.", call. = FALSE)
} else release <- ensembl_current_release(ensembl_summary$division[1])
if (is.numeric(release)) {
if (release <= 46) {
message("ensembl release <= 46 is not supported")
return(FALSE)
}
}
return(release)
}
#' Check if genome is available in ensembl
#' @param organism which organism, scientific name
#' @param details logical, default FALSE, return logical only, else table of info
#' @param division "EnsemblVertebrates", alternatives: "EnsemblPlants",
#' "EnsemblFungi", "EnsemblMetazoa" and "EnsemblProtists"
#' @return logical, if details is TRUE, then returns table of details.
#' @noRd
is.genome.available.ensembl <- function(db = "ensembl",
organism,
details = FALSE,
divisions = ensembl_divisions()) {
name <- accession <- accession <- assembly <- taxon_id <- NULL
new.organism <- stringr::str_replace_all(organism, " ", "_")
# For each ensembl division, check if it exists
for (division in ensembl_divisions()) {
ensembl.available.organisms <- get.ensembl.info(division = division)
ensembl.available.organisms <-
dplyr::filter(ensembl.available.organisms, !is.na(assembly))
if (!is.taxid(organism)) {
selected.organism <-
dplyr::filter(
ensembl.available.organisms,
stringr::str_detect(name,
stringr::str_to_lower(new.organism)) |
accession == organism,!is.na(assembly)
)
} else {
selected.organism <-
dplyr::filter(
ensembl.available.organisms,
taxon_id == as.integer(organism),!is.na(assembly)
)
}
if (nrow(selected.organism) > 0)
break
}
if (!details) {
if (nrow(selected.organism) == 0) {
organism_no_hit_message_zero(organism, db)
return(FALSE)
}
if (nrow(selected.organism) > 0) {
message("A reference or representative genome assembly is available for '",
organism,
"'.")
if (nrow(selected.organism) > 1) {
organism_no_hit_message_more_than_one(organism, db)
}
return(TRUE)
}
}
if (details)
return(selected.organism)
}
organism_no_hit_message_zero <- function(organism, db) {
message(
"Unfortunatey, no entry for '",
organism,
"' was found in the '",
db,
"' database. ",
"Please consider specifying ",
paste0("'db = ", dplyr::setdiff(
c("refseq", "genbank", "ensembl", "ensemblgenomes", "uniprot"),
db
), collapse = "' or "),
"' to check whether '",
organism,
"' is available in these databases."
)
}
organism_no_hit_message_more_than_one <- function(organism, db) {
message(
"More than one entry was found for '",
organism,
"'.",
" Please consider to run the function 'is.genome.available()' and specify 'is.genome.available(organism = ",
organism,
", db = ",
db,
", details = TRUE)'.",
" This will allow you to select the 'assembly_accession' identifier that can then be ",
"specified in all get*() functions."
)
}
#' Get ensembl collection info table
#'
#' @references https://ftp.ensemblgenomes.ebi.ac.uk/pub/README_metadata
#' @noRd
collection_table <- function(division = "EnsemblBacteria") {
base_name_file <- paste0(division, ".txt")
local_file <- file.path(tempdir(), base_name_file)
if (!file.exists(local_file)) {
url <- paste0(ensembl_ftp_server_url(division),"/",
ensembl_ftp_server_url_release(division),
"species_", base_name_file)
tryCatch({
custom_download(
url,
destfile = local_file,
mode = "wb"
)
}, error = function(e) {
message(
"Something went wrong when accessing the the file",
" Are you connected to the internet? ",
"Is the homepage '", url,"' ",
"currently available? Could it be that the scientific name is mis-spelled or includes special characters such as '.' or '('?"
)
})
}
collection <- suppressWarnings(data.table::fread(local_file))
colnames <- colnames(collection)[-1] # Remove false column
colnames[1] <- "name"
collection$species_id <- NULL
colnames(collection) <- colnames
if (!("core_db" %in% colnames)) stop("Loaded ensembl summary file is invalid,",
"is there changes we have not propogated to biomartr?",
"Please post an issue on github with species information")
return(collection)
}
get_collection_id <- function(ensembl_summary) {
division <- ensembl_summary$division[1]
if (!(division %in% c("EnsemblBacteria", "EnsemblFungi",
"EnsemblProtists")))
return("") # Only these have collection folder structure
get.org.info <- ensembl_summary[1,]
collection_info_full <- collection_table(division)
assembly <- assembly_accession <- NULL
collection_info <-
dplyr::filter(collection_info_full,
assembly == gsub("_$", "", get.org.info$assembly))
if (nrow(collection_info) == 0) {
# Special case for bacteria
collection_info <-
dplyr::filter(collection_info_full,
assembly_accession == get.org.info$accession)
if (nrow(collection_info) == 0) {
message(
"Unfortunately organism '",
ensembl_summary$display_name,
"' could not be found. Have you tried another database yet? ",
"E.g. db = 'ensembl'? Thus, download for this species is omitted."
)
return(FALSE)
}
}
collection <- collection_info$core_db[1]
split <- unlist(stringr::str_split(collection, "_"))[1:3]
is_not_collection <- (is.na(collection) || collection == "N") || split[3] != "collection"
if (is_not_collection) {
# TODO make sure this is safe (Currently that split[3] is collection might change!)
# In theory this should mean that the file exist outside collection folders
return("")
}
collection <- paste0(paste0(split, collapse = "_"), "/")
return(collection)
}
assembly_summary_and_rest_status <- function(organism) {
ensembl_summary <- ensembl_assembly_hits(organism)
if (isFALSE(ensembl_summary)) return(FALSE)
# Check if assembly can be reached (TODO: remove, as this is already done)
new.organism <- ensembl_proper_organism_name(ensembl_summary)
rest_url <- ensembl_rest_url_assembly(new.organism)
rest_api_status <- test_url_status(url = rest_url, organism = organism)
if (isFALSE(rest_api_status)) return(FALSE)
json.qry.info <- rest_api_status
return(list(new.organism = new.organism,
ensembl_summary = ensembl_summary,
json.qry.info = json.qry.info))
}
write_assembly_docs_ensembl <- function(genome.path, new.organism, db, json.qry.info,
path = dirname(genome.path[1]), append = NULL) {
# generate Genome documentation
sink(file.path(path, paste0("doc_", new.organism, "_db_", db, append,".txt")))
cat(paste0("File Name: ", genome.path[1]))
cat("\n")
cat(paste0("Download Path: ", genome.path[2]))
cat("\n")
cat(paste0("Organism Name: ", new.organism))
cat("\n")
cat(paste0("Database: ", db))
cat("\n")
cat(paste0("Download_Date: ", date()))
cat("\n")
cat(paste0("assembly_name: ", json.qry.info$assembly_name))
cat("\n")
cat(paste0("assembly_date: ", json.qry.info$assembly_date))
cat("\n")
cat(
paste0(
"genebuild_last_geneset_update: ",
json.qry.info$genebuild_last_geneset_update
)
)
cat("\n")
cat(paste0(
"assembly_accession: ",
json.qry.info$assembly_accession
))
cat("\n")
cat(
paste0(
"genebuild_initial_release_date: ",
json.qry.info$genebuild_initial_release_date
)
)
sink()
doc <- tibble::tibble(
file_name = genome.path[1],
download_path = genome.path[2],
organism = new.organism,
database = db,
download_data = date(),
assembly_name = ifelse(!is.null(json.qry.info$assembly_name), json.qry.info$assembly_name, "none"),
assembly_date = ifelse(!is.null(json.qry.info$assembly_date), json.qry.info$assembly_date, "none"),
genebuild_last_geneset_update = ifelse(!is.null(json.qry.info$genebuild_last_geneset_update), json.qry.info$genebuild_last_geneset_update, "none"),
assembly_accession = ifelse(!is.null(json.qry.info$assembly_accession), json.qry.info$assembly_accession, "none"),
genebuild_initial_release_date = ifelse(!is.null(json.qry.info$genebuild_initial_release_date), json.qry.info$genebuild_initial_release_date, "none")
)
readr::write_tsv(doc, file = file.path(
path,
paste0("doc_", new.organism, "_db_", db, append, ".tsv"))
)
return(invisible(NULL))
}
ensembl_download_post_processing <- function(genome.path, organism, format,
remove_annotation_outliers = FALSE,
gunzip = FALSE, db = "ensembl",
mute_citation = FALSE) {
if (genome.path[1] == "FALSE") {
return(FALSE)
} else {
# Format specific behaviors
if (format == "gtf") {append <- "_gtf_"} else append <- NULL
info <- assembly_summary_and_rest_status(organism)
write_assembly_docs_ensembl(genome.path, new.organism = info$new.organism,
db = db, json.qry.info = info$json.qry.info, append = append)
local_file <- genome.path[1]
gunzip_and_check(local_file, gunzip, remove_annotation_outliers, format, mute_citation)
}
}