Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
comparison 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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0:45755942ae7b | 1:9b4ee836e35b |
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1 ## | |
2 ## Run this script to update the table of Ensembl assemblies available in the customProDB annotation data manager (ensembl_datasets.loc) | |
3 ## | |
4 | |
5 library(RMySQL) | |
6 library(httr) | |
7 library(biomaRt) | |
8 library(stringdist) | |
9 | |
10 con = dbConnect(MySQL(), host="ensembldb.ensembl.org", user="anonymous") | |
11 archives = dbGetQuery(con, "SHOW DATABASES LIKE 'ensembl_archive_%'") | |
12 dbDisconnect(con) | |
13 | |
14 latestArchive = tail(archives[,1], 1) | |
15 con = dbConnect(MySQL(), host="ensembldb.ensembl.org", user="anonymous", dbname=latestArchive) | |
16 assemblies = dbGetQuery(con, "SELECT s.name, s.common_name, rs.assembly_name, MAX(rs.release_id) AS latest_release, r.date | |
17 FROM species as s, release_species as rs, ens_release as r | |
18 WHERE s.species_id = rs.species_id AND r.release_id = rs.release_id AND r.online = 'Y' | |
19 AND r.release_id < 10000 -- ignore 10075 (the special GRCh37 site) | |
20 GROUP BY rs.assembly_name | |
21 ORDER BY s.common_name, rs.release_id") | |
22 allReleases = assemblies$latest_release | |
23 uniqueReleases = unique(allReleases) | |
24 | |
25 # Get the <MMMYYYY> style archive link for each Ensembl release | |
26 urlRedirectMap = sapply(paste0("e", uniqueReleases, ".ensembl.org"), function(url){XML::parseURI(HEAD(url)$url)$server}) | |
27 | |
28 ## NOTE ## Make sure the following line is updated to the latest Ensembl mirror | |
29 assemblies$url = sub("www.", "may2017.archive.", urlRedirectMap[paste0("e", allReleases, ".ensembl.org")], fixed=TRUE) | |
30 | |
31 # Get all datasets from the archives | |
32 datasets = c() | |
33 for (archive in unique(assemblies$url)) { | |
34 datasets = unique(c(datasets, listDatasets(useMart("ensembl", host=archive))$dataset)) | |
35 } | |
36 datasets = sub("_gene_ensembl", "", datasets, fixed=TRUE) | |
37 | |
38 # Match the assembly species names to the datasets (using amatch() because of cases like Mustela_putorius_furo -> mfuro) | |
39 assemblies$dataset_id = datasets[amatch(tolower(assemblies$name), datasets, maxDist=3, method="osa", weight=c(0.1, 1, 1, 1))] | |
40 | |
41 # Remove mouse strains (would need to add these from ENSEMBL_MOUSE_MART) | |
42 assemblies = assemblies[-grep("Mus_musculus_\\S+", assemblies$name, perl=TRUE),] | |
43 | |
44 # Remove unmatched assemblies (e.g. Mus spretus) | |
45 assemblies = assemblies[-which(is.na(assemblies$dataset_id)),] | |
46 | |
47 # Replace underscores in scientific name | |
48 assemblies$name = gsub("_", " ", assemblies$name, fixed=TRUE) | |
49 | |
50 # Sort assemblies first by scientific name, then descending by latest release for that assembly | |
51 assemblies = assemblies[order(assemblies$name, -assemblies$latest_release),] | |
52 | |
53 # Write dataset table (3 columns: dataset_id, host, description) | |
54 dataset_id = paste0(assemblies$dataset_id, "_gene_ensembl") | |
55 host = paste0(assemblies$url) | |
56 description = paste0(assemblies$common_name, " genes (Ensembl ", assemblies$latest_release, " ", assemblies$dataset_id, | |
57 ") (", assemblies$assembly_name, ")") | |
58 write.csv(paste(dataset_id, host, description, sep="\t"), file="ensembl_datasets.loc.sample") |