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 testInfo() throws IOException {
// set a command line
CommandLine.setCommandArgs("aksfj", "-d", "djfk siduf");
try {
final ArrayList<InputStream> al = new ArrayList<>();
al.add(
createStream(
">123456789012345678901\nacgtgtgtgtcttagggctcactggtcatgca\n>bob-the-builder\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.setComment("wejksfd boier sakrjoieje");
sw.processSequences();
final CompressedMemorySequencesReader msr =
(CompressedMemorySequencesReader)
SequencesReaderFactory.createMemorySequencesReader(mDir, true, LongRange.NONE);
checkDetails(msr);
final CompressedMemorySequencesReader msr2 = (CompressedMemorySequencesReader) msr.copy();
assertTrue(msr2 != msr);
checkDetails(msr2);
assertEquals("wejksfd boier sakrjoieje", msr.comment());
assertEquals("wejksfd boier sakrjoieje", msr2.comment());
assertEquals("aksfj -d \"djfk siduf\"", msr.commandLine());
assertEquals("aksfj -d \"djfk siduf\"", msr2.commandLine());
} finally {
CommandLine.clearCommandArgs();
}
}
/**
* Alternative to other one with similar name
*
* @param directory directory containing SDF
* @param indexFile index file
* @param loadNames should we load names
* @param loadFullNames should we load full names
* @param region region to restrict to
* @throws IOException IO exception occurs
*/
CompressedMemorySequencesReader2(
File directory,
IndexFile indexFile,
boolean loadNames,
boolean loadFullNames,
LongRange region)
throws IOException {
mIndexFile = indexFile;
mRegion = SequencesReaderFactory.resolveRange(indexFile, region);
mStart = mRegion.getStart();
mEnd = mRegion.getEnd();
mNumberSequences = mEnd - mStart;
mData =
DataInMemory.loadDelayQuality(
directory,
indexFile,
DataFileIndex.loadSequenceDataFileIndex(indexFile.dataIndexVersion(), directory),
mStart,
mEnd);
if (mNumberSequences > Integer.MAX_VALUE) {
throw new IllegalArgumentException(
"Too many sequences in region: " + region + ", maximum is: " + Integer.MAX_VALUE);
}
mDirectory = directory;
if (loadNames && mIndexFile.hasNames()) {
loadNames();
loadNameSuffixes(loadFullNames, mIndexFile.hasSequenceNameSuffixes());
}
final StringBuilder sb = new StringBuilder("CMSR2 statistics");
sb.append(LS);
this.infoString(sb);
Diagnostic.userLog(sb.toString());
}
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});
}
}
