diff tool-data/update_ensembl_datasets.R @ 1:9b4ee836e35b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 2174137cf8a15deefed5910ffa152c4ce9c81af6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/update_ensembl_datasets.R	Thu Jun 08 10:55:08 2017 -0400
@@ -0,0 +1,58 @@
+##
+## Run this script to update the table of Ensembl assemblies available in the customProDB annotation data manager (ensembl_datasets.loc)
+##
+
+library(RMySQL)
+library(httr)
+library(biomaRt)
+library(stringdist)
+
+con = dbConnect(MySQL(), host="ensembldb.ensembl.org", user="anonymous")
+archives = dbGetQuery(con, "SHOW DATABASES LIKE 'ensembl_archive_%'")
+dbDisconnect(con)
+
+latestArchive = tail(archives[,1], 1)
+con = dbConnect(MySQL(), host="ensembldb.ensembl.org", user="anonymous", dbname=latestArchive)
+assemblies = dbGetQuery(con, "SELECT s.name, s.common_name, rs.assembly_name, MAX(rs.release_id) AS latest_release, r.date
+                              FROM species as s, release_species as rs, ens_release as r
+                              WHERE s.species_id = rs.species_id AND r.release_id = rs.release_id AND r.online = 'Y'
+                              AND r.release_id < 10000 -- ignore 10075 (the special GRCh37 site)
+                              GROUP BY rs.assembly_name
+                              ORDER BY s.common_name, rs.release_id")
+allReleases = assemblies$latest_release
+uniqueReleases = unique(allReleases)
+
+# Get the <MMMYYYY> style archive link for each Ensembl release
+urlRedirectMap = sapply(paste0("e", uniqueReleases, ".ensembl.org"), function(url){XML::parseURI(HEAD(url)$url)$server})
+
+## NOTE ## Make sure the following line is updated to the latest Ensembl mirror
+assemblies$url = sub("www.", "may2017.archive.", urlRedirectMap[paste0("e", allReleases, ".ensembl.org")], fixed=TRUE)
+
+# Get all datasets from the archives
+datasets = c()
+for (archive in unique(assemblies$url)) {
+    datasets = unique(c(datasets, listDatasets(useMart("ensembl", host=archive))$dataset))
+}
+datasets = sub("_gene_ensembl", "", datasets, fixed=TRUE)
+
+# Match the assembly species names to the datasets (using amatch() because of cases like Mustela_putorius_furo -> mfuro)
+assemblies$dataset_id = datasets[amatch(tolower(assemblies$name), datasets, maxDist=3, method="osa", weight=c(0.1, 1, 1, 1))]
+
+# Remove mouse strains (would need to add these from ENSEMBL_MOUSE_MART)
+assemblies = assemblies[-grep("Mus_musculus_\\S+", assemblies$name, perl=TRUE),]
+
+# Remove unmatched assemblies (e.g. Mus spretus)
+assemblies = assemblies[-which(is.na(assemblies$dataset_id)),]
+
+# Replace underscores in scientific name
+assemblies$name = gsub("_", " ", assemblies$name, fixed=TRUE)
+
+# Sort assemblies first by scientific name, then descending by latest release for that assembly
+assemblies = assemblies[order(assemblies$name, -assemblies$latest_release),]
+
+# Write dataset table (3 columns: dataset_id, host, description)
+dataset_id = paste0(assemblies$dataset_id, "_gene_ensembl")
+host = paste0(assemblies$url)
+description = paste0(assemblies$common_name, " genes (Ensembl ", assemblies$latest_release, " ", assemblies$dataset_id,
+                     ") (", assemblies$assembly_name, ")")
+write.csv(paste(dataset_id, host, description, sep="\t"), file="ensembl_datasets.loc.sample")