org.opencb.cellbase.lib.download.GenomeDownloadManager Maven / Gradle / Ivy
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/*
* Copyright 2015-2020 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.opencb.cellbase.lib.download;
import com.beust.jcommander.ParameterException;
import org.apache.commons.lang.StringUtils;
import org.opencb.cellbase.core.config.CellBaseConfiguration;
import org.opencb.cellbase.core.exception.CellBaseException;
import org.opencb.cellbase.lib.EtlCommons;
import org.opencb.commons.utils.DockerUtils;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.*;
public class GenomeDownloadManager extends AbstractDownloadManager {
private static final String ENSEMBL_NAME = "ENSEMBL";
private static final String GERP_NAME = "GERP++";
private static final String PHASTCONS_NAME = "PhastCons";
private static final String PHYLOP_NAME = "PhyloP";
private static final String TRF_NAME = "Tandem repeats finder";
private static final String GSD_NAME = "Genomic super duplications";
private static final String WM_NAME = "WindowMasker";
public GenomeDownloadManager(String species, String assembly, Path targetDirectory, CellBaseConfiguration configuration)
throws IOException, CellBaseException {
super(species, assembly, targetDirectory, configuration);
}
@Override
public List download() throws IOException, InterruptedException {
List downloadFiles = new ArrayList<>();
downloadFiles.addAll(downloadReferenceGenome());
// downloadFiles.addAll(downloadConservation());
// downloadFiles.addAll(downloadRepeats());
// cytobands
runGenomeInfo();
return downloadFiles;
}
public List downloadReferenceGenome() throws IOException, InterruptedException {
logger.info("Downloading genome information ...");
Path sequenceFolder = downloadFolder.resolve("genome");
Files.createDirectories(sequenceFolder);
// Reference genome sequences are downloaded from Ensembl
// New Homo sapiens assemblies contain too many ALT regions, so we download 'primary_assembly' file instead
String url = ensemblHostUrl + "/" + ensemblRelease;
if (speciesConfiguration.getScientificName().equals("Homo sapiens")) {
url = url + "/fasta/" + speciesShortName + "/dna/*.dna.primary_assembly.fa.gz";
} else {
if (!configuration.getSpecies().getVertebrates().contains(speciesConfiguration)) {
url = ensemblHostUrl + "/" + ensemblRelease + "/" + getPhylo(speciesConfiguration);
}
url = url + "/fasta/";
if (configuration.getSpecies().getBacteria().contains(speciesConfiguration)) {
// WARN: assuming there's just one assembly
url = url + speciesConfiguration.getAssemblies().get(0).getEnsemblCollection() + "/";
}
url = url + speciesShortName + "/dna/*.dna.toplevel.fa.gz";
}
String outputFileName = StringUtils.capitalize(speciesShortName) + "." + assemblyConfiguration.getName() + ".fa.gz";
Path outputPath = sequenceFolder.resolve(outputFileName);
logger.info("Saving reference genome version data at {}", sequenceFolder.resolve("genomeVersion.json"));
saveVersionData(EtlCommons.GENOME_DATA, ENSEMBL_NAME, ensemblVersion, getTimeStamp(),
Collections.singletonList(url), sequenceFolder.resolve("genomeVersion.json"));
List downloadFiles = Collections.singletonList(downloadFile(url, outputPath.toString()));
logger.info("Unzipping file: " + outputFileName);
EtlCommons.runCommandLineProcess(null, "gunzip", Collections.singletonList(outputPath.toString()), null);
return downloadFiles;
}
/**
* This method downloads bith PhastCons and PhyloP data from UCSC for Human and Mouse species.
* @return list of files downloaded
* @throws IOException if there is an error writing to a file
* @throws InterruptedException if there is an error downloading files
*/
public List downloadConservation() throws IOException, InterruptedException {
if (!speciesHasInfoToDownload(speciesConfiguration, "conservation")) {
return null;
}
logger.info("Downloading conservation information ...");
Path conservationFolder = downloadFolder.resolve("conservation");
List downloadFiles = new ArrayList<>();
if (speciesConfiguration.getScientificName().equals("Homo sapiens")) {
Files.createDirectories(conservationFolder);
Files.createDirectories(conservationFolder.resolve("gerp"));
Files.createDirectories(conservationFolder.resolve("phastCons"));
Files.createDirectories(conservationFolder.resolve("phylop"));
String[] chromosomes = {"1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
"15", "16", "17", "18", "19", "20", "21", "22", "X", "Y", "M", };
if (assemblyConfiguration.getName().equalsIgnoreCase("GRCh38")) {
String url = configuration.getDownload().getConservation().getHost() + "/hg38";
List phastconsUrls = new ArrayList<>(chromosomes.length);
List phyloPUrls = new ArrayList<>(chromosomes.length);
for (String chromosome : chromosomes) {
String phastConsUrl = url + "/phastCons100way/hg38.100way.phastCons/chr" + chromosome
+ ".phastCons100way.wigFix.gz";
downloadFiles.add(downloadFile(phastConsUrl, conservationFolder.resolve("phastCons")
.resolve("chr" + chromosome + ".phastCons100way.wigFix.gz").toString()));
phastconsUrls.add(phastConsUrl);
String phyloPUrl = url + "/phyloP100way/hg38.100way.phyloP100way/chr" + chromosome
+ ".phyloP100way.wigFix.gz";
downloadFiles.add(downloadFile(phyloPUrl, conservationFolder.resolve("phylop")
.resolve("chr" + chromosome + ".phyloP100way.wigFix.gz").toString()));
phyloPUrls.add(phyloPUrl);
}
String gerpUrl = configuration.getDownload().getGerp().getHost();
downloadFiles.add(downloadFile(gerpUrl, conservationFolder.resolve(EtlCommons.GERP_SUBDIRECTORY)
.resolve(EtlCommons.GERP_FILE).toString()));
saveVersionData(EtlCommons.CONSERVATION_DATA, GERP_NAME, null, getTimeStamp(), Collections.singletonList(gerpUrl),
conservationFolder.resolve("gerpVersion.json"));
saveVersionData(EtlCommons.CONSERVATION_DATA, PHASTCONS_NAME, null, getTimeStamp(), phastconsUrls,
conservationFolder.resolve("phastConsVersion.json"));
saveVersionData(EtlCommons.CONSERVATION_DATA, PHYLOP_NAME, null, getTimeStamp(), phyloPUrls,
conservationFolder.resolve("phyloPVersion.json"));
}
}
if (speciesConfiguration.getScientificName().equals("Mus musculus")) {
Files.createDirectories(conservationFolder);
Files.createDirectories(conservationFolder.resolve("phastCons"));
Files.createDirectories(conservationFolder.resolve("phylop"));
String url = configuration.getDownload().getConservation().getHost() + "/mm10";
String[] chromosomes = {"1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
"15", "16", "17", "18", "19", "X", "Y", "M", };
List phastconsUrls = new ArrayList<>(chromosomes.length);
List phyloPUrls = new ArrayList<>(chromosomes.length);
for (String chromosome : chromosomes) {
String phastConsUrl = url + "/phastCons60way/mm10.60way.phastCons/chr" + chromosome + ".phastCons60way.wigFix.gz";
downloadFiles.add(downloadFile(phastConsUrl, conservationFolder.resolve("phastCons").resolve("chr" + chromosome
+ ".phastCons60way.wigFix.gz").toString()));
phastconsUrls.add(phastConsUrl);
String phyloPUrl = url + "/phyloP60way/mm10.60way.phyloP60way/chr" + chromosome + ".phyloP60way.wigFix.gz";
downloadFiles.add(downloadFile(phyloPUrl, conservationFolder.resolve("phylop").resolve("chr" + chromosome
+ ".phyloP60way.wigFix.gz").toString()));
phyloPUrls.add(phyloPUrl);
}
saveVersionData(EtlCommons.CONSERVATION_DATA, PHASTCONS_NAME, null, getTimeStamp(), phastconsUrls,
conservationFolder.resolve("phastConsVersion.json"));
saveVersionData(EtlCommons.CONSERVATION_DATA, PHYLOP_NAME, null, getTimeStamp(), phyloPUrls,
conservationFolder.resolve("phastConsVersion.json"));
}
return downloadFiles;
}
public List downloadRepeats() throws IOException, InterruptedException {
if (!speciesHasInfoToDownload(speciesConfiguration, "repeats")) {
return null;
}
if (speciesConfiguration.getScientificName().equals("Homo sapiens")) {
logger.info("Downloading repeats data ...");
Path repeatsFolder = downloadFolder.resolve(EtlCommons.REPEATS_FOLDER);
Files.createDirectories(repeatsFolder);
List downloadFiles = new ArrayList<>();
String pathParam;
if (assemblyConfiguration.getName().equalsIgnoreCase("grch38")) {
pathParam = "hg38";
} else {
logger.error("Please provide a valid human assembly {GRCh37, GRCh38)");
throw new ParameterException("Assembly '" + assemblyConfiguration.getName() + "' is not valid. Please provide "
+ "a valid human assembly {GRCh37, GRCh38)");
}
// Download tandem repeat finder
String url = configuration.getDownload().getSimpleRepeats().getHost() + "/" + pathParam
+ "/database/simpleRepeat.txt.gz";
downloadFiles.add(downloadFile(url, repeatsFolder.resolve(EtlCommons.TRF_FILE).toString()));
saveVersionData(EtlCommons.REPEATS_DATA, TRF_NAME, null, getTimeStamp(), Collections.singletonList(url),
repeatsFolder.resolve(EtlCommons.TRF_VERSION_FILE));
// Download genomic super duplications
url = configuration.getDownload().getGenomicSuperDups().getHost() + "/" + pathParam
+ "/database/genomicSuperDups.txt.gz";
downloadFiles.add(downloadFile(url, repeatsFolder.resolve(EtlCommons.GSD_FILE).toString()));
saveVersionData(EtlCommons.REPEATS_DATA, GSD_NAME, null, getTimeStamp(), Collections.singletonList(url),
repeatsFolder.resolve(EtlCommons.GSD_VERSION_FILE));
// Download WindowMasker
if (!pathParam.equalsIgnoreCase("hg19")) {
url = configuration.getDownload().getWindowMasker().getHost() + "/" + pathParam
+ "/database/windowmaskerSdust.txt.gz";
downloadFiles.add(downloadFile(url, repeatsFolder.resolve(EtlCommons.WM_FILE).toString()));
saveVersionData(EtlCommons.REPEATS_DATA, WM_NAME, null, getTimeStamp(), Collections.singletonList(url),
repeatsFolder.resolve(EtlCommons.WM_VERSION_FILE));
}
return downloadFiles;
}
return null;
}
public void runGenomeInfo() throws IOException, InterruptedException {
logger.info("Downloading genome info ...");
// TODO don't run this if file already exists
String outputFolder = downloadFolder.getParent().toAbsolutePath().toString() + "/generated_json/";
if ("true".equals(System.getenv("CELLBASE_BUILD_DOCKER"))) {
String outputLog = downloadLogFolder + "/genome_info.log";
EtlCommons.runCommandLineProcess(null, "/opt/cellbase/genome_info.pl",
Arrays.asList("--outdir", outputFolder),
outputLog);
} else {
String dockerImage = "opencb/cellbase-builder:" + configuration.getApiVersion();
AbstractMap.SimpleEntry outputBinding = new AbstractMap.SimpleEntry(outputFolder, "/ensembl-data");
String ensemblScriptParams = "/opt/cellbase/genome_info.pl";
DockerUtils.run(dockerImage, null, outputBinding, ensemblScriptParams, null);
}
}
}
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