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* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package org.broad.igv.feature.genome;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.io.File;
import java.io.FilenameFilter;
import java.util.zip.ZipFile;
import static junit.framework.Assert.*;
/**
* User: jacob
* Date: 2012-Sep-06
*/
public class GenomeImporterTest extends AbstractHeadlessTest {
@Test
public void testCreateGenomeArchiveFromDir() throws Exception {
File genomeFile = new File(TestUtils.DATA_DIR, "out/testSetGenome.genome");
String genomeId = "testSet";
String genomeDisplayName = genomeId;
String fastaPath = TestUtils.DATA_DIR + "fasta/set";
deleteFaiFiles(fastaPath);
File genomeArchive = (new GenomeImporter()).createGenomeArchive(
genomeFile, genomeId, genomeDisplayName, fastaPath,
null, null, null);
assertNotNull(genomeArchive);
assertTrue(genomeArchive.exists());
deleteFaiFiles(fastaPath);
}
@Test
public void testCreateGenomeArchiveFromFiles() throws Exception {
File genomeFile = new File(TestUtils.DATA_DIR, "out/testSetGenome.genome");
String genomeId = "testSet";
String genomeDisplayName = genomeId;
String fastaPath = TestUtils.DATA_DIR + "fasta/ecoli_out.padded.fasta";
File fastaFile = new File(fastaPath);
String parentDir = TestUtils.DATA_DIR + "genomes/genome_raw_files/hg18.unittest";
File cytobandFile = new File(parentDir, "hg18_cytoBand.txt");
File geneAnnotFile = new File(parentDir, "hg18_refGene_head1k.txt");
File chrAliasFile = new File(parentDir, "pointless_alias.tab");
deleteFaiFiles(fastaPath);
File genomeArchive = (new GenomeImporter()).createGenomeArchive(
genomeFile, genomeId, genomeDisplayName, fastaPath,
geneAnnotFile, cytobandFile, chrAliasFile);
assertNotNull(genomeArchive);
assertTrue(genomeArchive.exists());
GenomeDescriptor descriptor = GenomeManager.getInstance().parseGenomeArchiveFile(genomeArchive);
assertEquals(cytobandFile.getName(), descriptor.cytoBandFileName);
assertEquals(geneAnnotFile.getName(), descriptor.getGeneFileName());
assertEquals(chrAliasFile.getName(), descriptor.chrAliasFileName);
assertEquals(fastaFile.getAbsolutePath(), descriptor.getSequenceLocation());
assertTrue(descriptor.hasCytobands());
assertTrue(descriptor.isChromosomesAreOrdered());
assertTrue(descriptor.isFasta());
//Check that files seem to be accurate. We just look at sizes
ZipFile zipFile = new ZipFile(genomeArchive);
File[] files = new File[]{cytobandFile, geneAnnotFile, chrAliasFile};
for(File file: files){
assertEquals("File sizes unequal for " + file.getName(), file.length(), zipFile.getEntry(file.getName()).getSize());
}
deleteFaiFiles(fastaPath);
}
/**
* Deletes all fasta index files in the provided path
*
* @param dir
*/
private void deleteFaiFiles(String dir) {
//Delete index files, if they exist
File fastaDir = new File(dir);
File[] idxFiles = fastaDir.listFiles(new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
return name.endsWith(".fai");
}
});
if(idxFiles == null) return;
for (File idxFile : idxFiles) {
idxFile.delete();
}
}
}