@Test
public void testGetCluster() throws IOException {
System.out.println("Get all the genes around BRCA1");
String[] paths = {"gene"};
String query = "x\ty\tz\t{\"_landmark\":\"17\",\"_minBP\":41166622,\"_maxBP\":41297272}";
OverlapPipe op = new OverlapPipe(geneFile, 0, 0);
Pipe p = new Pipeline(new HistoryInPipe(), op, new DrillPipe(false, paths), new PrintPipe());
p.setStarts(Arrays.asList(query));
for (int i = 1; p.hasNext(); i++) {
History h = (History) p.next();
if (i == 1) {
assertEquals("VAT1", h.get(4));
}
if (i == 2) {
assertEquals("RND2", h.get(4));
}
if (i == 3) {
assertEquals("BRCA1", h.get(4));
}
if (i == 4) {
assertEquals("RPL21P4", h.get(4));
}
if (i == 5) {
assertEquals("NBR2", h.get(4));
}
if (i == 6) {
assertEquals("LOC100505873", h.get(4));
}
if (i == 7) {
assertEquals("HMGN1P29", h.get(4));
}
}
}
@Override
protected History processNextStart() throws NoSuchElementException {
if (this.starts.hasNext()) {
History history = this.starts.next();
for (int i = 0; i < history.size(); i++) {
String value = history.get(i) + mSuffix;
history.set(i, value);
}
return history;
} else {
throw new NoSuchElementException();
}
}
@Test
public void testBRCA1DOWN() throws IOException {
System.out.println("Get the genes down-chromosome and including BRCA1");
String[] paths = {"gene"};
String query = "x\ty\tz\t" + BRCA1;
OverlapPipe op = new OverlapPipe(geneFile, 0, 19772);
Pipe p = new Pipeline(new HistoryInPipe(), op, new DrillPipe(false, paths), new PrintPipe());
p.setStarts(Arrays.asList(query));
for (int i = 1; p.hasNext(); i++) {
History h = (History) p.next();
if (i == 1) {
assertEquals("BRCA1", h.get(4));
}
if (i == 2) {
assertEquals("RPL21P4", h.get(4)); // gene overlaps BRCA1 so it is included
}
if (i == 3) {
assertEquals("NBR2", h.get(4));
}
if (i == 4) {
assertEquals("LOC100505873", h.get(4));
}
if (i == 5) {
assertEquals("HMGN1P29", h.get(4));
}
}
}