public void testWorks() throws Exception {
try (TestDirectory dir = new TestDirectory("sdf2fasta")) {
final File xd = new File(dir, "sdf");
final ArrayList<InputStream> al = new ArrayList<>();
al.add(
new ByteArrayInputStream(
">test\nacgt\n>bob\ntagt\naccc\n>cat\ncat\n>dog\nccc".getBytes()));
final FastaSequenceDataSource ds = new FastaSequenceDataSource(al, new DNAFastaSymbolTable());
final SequencesWriter sw = new SequencesWriter(ds, xd, 300000, PrereadType.UNKNOWN, false);
sw.processSequences();
File x;
SequencesReader sr = SequencesReaderFactory.createDefaultSequencesReader(xd);
try {
x = new File(dir, "junitmy.fasta");
checkMainInitOk("-i", xd.toString(), "-o", x.toString(), "-Z");
checkContent1(x);
} finally {
sr.close();
}
sr = SequencesReaderFactory.createDefaultSequencesReader(xd);
try {
checkMainInitOk("-i", xd.toString(), "-o", x.toString(), "-l", "3", "-Z");
checkContent2(x);
} finally {
sr.close();
}
}
}
public void testRoll() throws Exception {
final ArrayList<InputStream> al = new ArrayList<>();
al.add(
createStream(
">123456789012345678901\nacgtgtgtgtcttagggctcactggtcatgca\n>bob the buuilder\ntagttcagcatcgatca\n>hobos r us\naccccaccccacaaacccaa"));
final FastaSequenceDataSource ds = new FastaSequenceDataSource(al, new DNAFastaSymbolTable());
final SequencesWriter sw = new SequencesWriter(ds, mDir, 20, PrereadType.UNKNOWN, false);
sw.processSequences();
try (SequencesReader dsr =
SequencesReaderFactory.createMemorySequencesReader(mDir, true, LongRange.NONE)) {
final SequencesIterator it = dsr.iterator();
assertTrue(((CompressedMemorySequencesReader) dsr).integrity());
assertEquals(mDir, dsr.path());
assertTrue(it.nextSequence());
assertEquals("1234567890123456789", it.currentName());
assertEquals(32, it.currentLength());
SequencesWriterTest.checkEquals(
it,
new byte[] {
1, 2, 3, 4, 3, 4, 3, 4, 3, 4, 2, 4, 4, 1, 3, 3, 3, 2, 4, 2, 1, 2, 4, 3, 3, 4, 2, 1, 4,
3, 2, 1
});
assertTrue(it.nextSequence());
assertEquals("bob", it.currentName());
assertEquals(17, it.currentLength());
SequencesWriterTest.checkEquals(
it, new byte[] {4, 1, 3, 4, 4, 2, 1, 3, 2, 1, 4, 2, 3, 1, 4, 2, 1});
assertTrue(it.nextSequence());
assertEquals("hobos", it.currentName());
assertEquals(20, it.currentLength());
SequencesWriterTest.checkEquals(
it, new byte[] {1, 2, 2, 2, 2, 1, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 1});
}
}
public void testEmptyFasta() throws IOException {
final SequencesReader reader = ReaderTestUtils.getReaderDNA("", mDir, new SdfId(0L));
reader.close();
final CompressedMemorySequencesReader cmsr =
new CompressedMemorySequencesReader(
mDir, new IndexFile(mDir), 5, true, false, new LongRange(0, 0));
assertEquals(0, cmsr.numberSequences());
}
public void testOverEndFastq() throws Exception {
final SequencesReader reader = ReaderTestUtils.getReaderDNAFastq(POSITIONS_FASTQ, mDir, false);
reader.close();
new CompressedMemorySequencesReader(
mDir, new IndexFile(mDir), 5, true, false, new LongRange(3, 8));
// Now this is OK rather than Exception, since our std behaviour is to warn and clip end that
// are too high back to the available num seqs
}
public void testFastqEnd() throws Exception {
final SequencesReader reader =
ReaderTestUtils.getReaderDNAFastq(POSITIONS_FASTQ, mDir, 20, false);
reader.close();
final SequencesIterator cmsr =
new CompressedMemorySequencesReader(
mDir, new IndexFile(mDir), 5, true, false, new LongRange(5, 6))
.iterator();
cmsr.nextSequence();
checkFastq(cmsr, "r5", "ACGTAC");
assertFalse(cmsr.nextSequence());
}
public void testRanges() throws Exception {
final SequencesReader reader = ReaderTestUtils.getReaderDNAFastq(SMALL_FASTQ, mDir, 20, false);
reader.close();
final CompressedMemorySequencesReader cmsr =
new CompressedMemorySequencesReader(
mDir, new IndexFile(mDir), 5, true, false, LongRange.NONE);
final byte[] foo = new byte[6];
cmsr.readQuality(0, foo, 4, 6);
final String qual = "EFGHIJ";
for (int i = 0; i < foo.length; i++) {
assertEquals(qual.charAt(i) - '!', foo[i]);
}
}
