public void wirteChainsIntoAGffFile(
ArrayList<Double> PDScores, String blockId, String pathToChainsDir, double scoreThreshold)
throws IOException {
String blockSpecfications[] = blockId.split("_");
String Chr = blockSpecfications[0];
String gffoutputFileName = pathToChainsDir + "/" + blockId + ".gff";
PrintWriter pw = new PrintWriter(new FileWriter(gffoutputFileName));
final GFFWriter gffw = new GFFWriter(pw);
int numberOfPDScores = PDScores.size();
int oneStart = 0;
int oneEnd = 0;
int dummyPos = 0;
for (int i = 0; i < numberOfPDScores - 1; i++) {
double thisScore = PDScores.get(i);
double nextScore = PDScores.get(i + 1);
if (PDScores.get(0) >= scoreThreshold) {
thisScore = thisScore - 0.001;
}
if (thisScore < scoreThreshold && nextScore >= scoreThreshold) {
oneStart = i + 1;
dummyPos = i + 1;
double sum = 0;
while (PDScores.get(dummyPos) >= scoreThreshold && dummyPos < numberOfPDScores - 1) {
sum = sum + PDScores.get(dummyPos + 1);
dummyPos++;
} /*while*/
// System.out.println(" start = " + oneStart + " end = " + dummyPos);
oneEnd = dummyPos;
int oneChainLength = oneEnd - oneStart;
SimpleGFFRecord oneRecord = new SimpleGFFRecord();
oneRecord.setStart(oneStart + 1);
oneRecord.setEnd(oneEnd);
oneRecord.setSeqName(Chr);
oneRecord.setScore(sum / oneChainLength); // oneRecord.setScore(sum/oneChainLength+1);
oneRecord.setSource("composure");
oneRecord.setFeature("chainFromPD");
int minChainLength = getMinPeakLengths();
if (oneChainLength > 5) {
// System.out.println(Chr + "\t" + oneStart + "\t" + oneEnd + "\t" + oneChainLength);
gffw.recordLine(oneRecord);
}
i = oneEnd - 1;
} /*if*/
} /*for*/
pw.flush();
} /*wirteChainsIntoAGffFile*/
/**
* @param args
* @throws Exception
*/
public void main(String[] args) throws Exception {
List<Map<String, Location>> locs = new ArrayList<Map<String, Location>>();
for (String fileName : args) {
locs.add(GFFUtils.gffToLocationMap(new File(fileName)));
}
Set<String> seqIds;
{
Iterator<Map<String, Location>> i = locs.iterator();
seqIds = new HashSet<String>(i.next().keySet());
while (i.hasNext()) {
seqIds.retainAll(i.next().keySet());
}
}
if (validate && (seqDB != null)) {
for (Map<String, Location> ls : locs) {
WriteCoveredSequences.validateGFFSequenceIdentifiersAgainstSequences(ls, seqDB);
}
}
PrintWriter pw = null;
GFFWriter gffw = null;
GFFEntrySet gffEntries = null;
if (outputFormat == Format.GFF) {
pw = new PrintWriter(new OutputStreamWriter(System.out));
gffw = new GFFWriter(pw);
} else {
gffEntries = new GFFEntrySet();
}
for (String id : seqIds) {
Iterator<Map<String, Location>> i = locs.iterator();
Location l = i.next().get(id);
while (i.hasNext()) {
l = LocationTools.intersection(l, i.next().get(id));
}
if (negate) {
l = LocationTools.subtract(new RangeLocation(1, seqDB.getSequence(id).length()), l);
}
SimpleGFFRecord r = new SimpleGFFRecord();
r.setSeqName(id);
r.setFeature("block");
r.setSource("nmintersectseq");
r.setStrand(StrandedFeature.POSITIVE);
for (Iterator<?> bi = l.blockIterator(); bi.hasNext(); ) {
Location bloc = (Location) bi.next();
r.setStart(bloc.getMin());
r.setEnd(bloc.getMax());
r.setComment("");
r.setGroupAttributes(new HashMap<Object, Object>());
if (gffw != null) {
gffw.recordLine(r);
} else {
Sequence seq =
new SimpleSequence(
seqDB.getSequence(id).subList(bloc.getMin(), bloc.getMax()),
null,
String.format("%s_|%d-%d|", id, bloc.getMin(), bloc.getMax()),
Annotation.EMPTY_ANNOTATION);
RichSequence.IOTools.writeFasta(System.out, seq, null);
}
}
}
if (pw != null) pw.flush();
if (seqDB != null) {
System.err.println("Writing output sequences...");
GFFTools.annotateSequences(seqDB, gffEntries);
}
}