public void testTaxonomySDF() throws IOException { try (final TestDirectory dir = new TestDirectory("sdfstats")) { // One without tax final File smallSdf = ReaderTestUtils.getDNADir(dir); final String err = checkMainInitBadFlags("-i", smallSdf.getPath(), "-o", "-", "--taxons", "41431"); TestUtils.containsAll(err, "does not contain taxonomy"); // One with tax final File fullSdf = new File(dir, "sdf_full"); final File faOut = new File(dir, "ex.fasta.gz"); makeTestTaxonSdf(fullSdf); checkMainInitOk("-i", fullSdf.getPath(), "-o", faOut.getPath(), "--taxons", "41431"); final String faout = FileHelper.gzFileToString(faOut); TestUtils.containsAll( faout, "gi|218169684|gb|CP001289.1|", "gi|218165370|gb|CP001287.1|", "gi|218169729|gb|CP001290.1|", "gi|218169631|gb|CP001288.1|"); } }
public void testFullName() throws IOException { try (TestDirectory dir = new TestDirectory("sdf2fasta")) { final File sdf = ReaderTestUtils.getDNADir(FULL_NAME_DATA, new File(dir, "sdf")); final File fasta = new File(dir, "fs.fasta.gz"); checkMainInitOk("-i", sdf.getPath(), "-o", fasta.getPath()); assertEquals(FULL_NAME_DATA, FileHelper.gzFileToString(fasta)); } }