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));
}
}
