Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
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
author | galaxyp |
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date | Thu, 08 Jun 2017 10:55:08 -0400 |
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--- /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")