/** calculates statstics and output for results on a given test sequence */
public void calcResultIncrement(TrainingSequence training, int[] predictedHiddenSequence) {
labeled.add(
new TrainingSequence(
training.getInputSequence(),
predictedHiddenSequence)); // This is only place that labelled gets added to???
// So I guess the results just get built up incrementally, both the actuall hidden sequences and
// the stats?
Assert.a(training.length() == predictedHiddenSequence.length);
int[] actualHiddenSequence = new int[training.length()];
for (int i = 0; i < training.length(); i++) {
actualHiddenSequence[i] = training.getY(i);
}
boolean thisperfect = true;
for (int i = 0; i < predictedHiddenSequence.length; ++i) {
int predY = predictedHiddenSequence[i];
int realY = actualHiddenSequence[i];
if (realY == predY) {
correct += 1;
} else {
incorrect += 1;
thisperfect = false;
}
ctCodingNucleotide.increment(isCodingPlus(predY), isCodingPlus(realY));
ctCodingNucleotide.increment(isCodingMinus(predY), isCodingMinus(realY));
for (int s = 0; s < nStates; s++) {
ctStates.get(s).increment((predY == s), (realY == s));
}
}
if (thisperfect) {
perfect++;
} else {
imperfect++;
}
for (int i = 1; i < predictedHiddenSequence.length; ++i) {
int predY = predictedHiddenSequence[i];
int realY = actualHiddenSequence[i];
int predYp = predictedHiddenSequence[i - 1];
int realYp = actualHiddenSequence[i - 1];
for (int t = 0; t < nTransitions; t++) {
boolean bPred = ((predYp == fromInd.get(t)) && (predY == toInd.get(t)));
boolean bReal = ((realYp == fromInd.get(t)) && (realY == toInd.get(t)));
ctTransitions.get(t).increment(bPred, bReal);
}
}
// Now let's increment the contingency table for exons; note that here not counting TN's
RangeMap predExonsPlus = new RangeMap();
RangeMap predExonsMinus = new RangeMap();
RangeMap realExonsPlus = new RangeMap();
RangeMap realExonsMinus = new RangeMap();
makeExonRangeMapFrom13SV(predictedHiddenSequence, predExonsPlus, predExonsMinus);
makeExonRangeMapFrom13SV(actualHiddenSequence, realExonsPlus, realExonsMinus);
incrementCTFromRangeMaps(ctExons, predExonsPlus, realExonsPlus);
incrementCTFromRangeMaps(ctExons, predExonsMinus, realExonsMinus);
}
private void parseSeqName(TrainingSequence seq, int seqNum) {
NameInputSequence nameInput = null;
InputSequence<?> inputSeq = seq.getInputSequence();
if (inputSeq instanceof InputSequenceComposite) {
nameInput = (NameInputSequence) inputSeq.getComponent("name");
}
if (nameInput == null) {
log.debug(
"Sequence name not specified. Setting sequence name to 'SEQ_"
+ String.valueOf(seqNum)
+ "'");
seqName = "SEQ_" + String.valueOf(seqNum); // Create a name and return.
genePrefix = "SEQ_" + String.valueOf(seqNum);
offset = 0;
return;
}
String name = nameInput.getName().trim();
int colon1, colon2, numColons;
if (name.startsWith("group:") || name.startsWith("seq:")) {
numColons = numOccurrences(name, ':');
if (numColons == 1) {
colon1 = name.indexOf(":");
seqName = name;
genePrefix = name.substring(colon1 + 1, name.length());
offset = 0;
return;
} else if (numColons == 2) {
colon1 = name.indexOf(":");
colon2 = name.lastIndexOf(":");
seqName = name.substring(0, colon2);
genePrefix = name.substring(colon1 + 1, colon2);
int pound = genePrefix.indexOf("#");
if (pound > 0) {
genePrefix = genePrefix.substring(0, pound);
}
setOffset(name.substring(colon2 + 1, name.length()));
return;
}
}
log.debug(
"Sequence name is in unexpected format. Setting offset=0 and sequence name='"
+ name
+ "'.");
seqName = name;
genePrefix = name;
offset = 0;
}
// This function converts a 13 state model hidden sequence to a GTF file.
public void writeGTF(List<? extends TrainingSequence<?>> refStates, String filename)
throws IOException {
int ref, geneNum, seqCount, frame = -1;
long i, exonStart, exonEnd, end;
boolean inPlusExon, inMinusExon, firstExon, startCodonSplit;
String strand;
Writer fout = new BufferedWriter(new FileWriter(filename));
exonStart = exonEnd = 0;
geneNum = 1;
seqCount = 0;
// Determine if model is tricycle13 or interval13.
boolean interval13 = false;
int prevState, state;
for (TrainingSequence seq : refStates) {
if (seq.length() == 0) continue;
prevState = seq.getY(0);
for (i = 1; i < seq.length(); i++) {
state = seq.getY((int) i);
if (prevState == 0 && (state == 2 || state == 3 || state == 7 || state == 8)) {
interval13 = true;
break;
}
prevState = state;
}
if (interval13) break;
}
for (TrainingSequence seq : refStates) {
if (interval13) {
SequenceConverter.convertSeqFromInterval13ToTricycle13(seq);
}
inPlusExon = false;
inMinusExon = false;
firstExon = true;
startCodonSplit = false;
parseSeqName(seq, seqCount);
for (i = 0; i < seq.length(); i++) {
ref = seq.getY((int) i);
if (ref == 1 || ref == 2 || ref == 3) // in a plus exon
{
if (!inPlusExon) {
exonStart = i + 1;
inPlusExon = true;
frame = setFrame(ref);
}
} else if (ref == 7 || ref == 8 || ref == 9) // in a minus exon
{
if (!inMinusExon) {
exonStart = i + 1;
inMinusExon = true;
frame = setFrame(ref);
if (firstExon) {
if (i < 3)
System.err.println(
"Minus strand gene start is within 3 nucleotides of sequence start. No stop codon writen to GTF for gene starting at position "
+ (exonStart + offset));
else
writeGFTLine(
fout,
seqName,
"stop_codon",
exonStart + offset - 3,
exonStart + offset - 1,
"-",
frame,
genePrefix,
geneNum);
}
}
} else if (inPlusExon
&& (ref == 4 || ref == 5
|| ref == 6)) { // just ended an exon on plus strand, now in a plus intron
strand = "+";
inPlusExon = false;
exonEnd = i;
if (firstExon) {
if (exonEnd - exonStart + 1 < 3) {
end = exonEnd + offset;
startCodonSplit = true;
} else {
end = exonStart + offset + 2;
}
writeGFTLine(
fout,
seqName,
"start_codon",
exonStart + offset,
end,
strand,
frame,
genePrefix,
geneNum);
firstExon = false;
} else if (startCodonSplit) { // at second exon that contains part of start codon
Assert.a(frame == 1 || frame == 2);
writeGFTLine(
fout,
seqName,
"start_codon",
exonStart + offset,
exonStart + offset + frame - 1,
strand,
frame,
genePrefix,
geneNum);
startCodonSplit = false;
}
writeGFTLine(
fout,
seqName,
"CDS",
exonStart + offset,
exonEnd + offset,
strand,
frame,
genePrefix,
geneNum);
} else if (inMinusExon
&& (ref == 10 || ref == 11
|| ref == 12)) { // just ended an exon on minus strand, now in a minus intron
strand = "-";
inMinusExon = false;
firstExon = false;
exonEnd = i;
writeGFTLine(
fout,
seqName,
"CDS",
exonStart + offset,
exonEnd + offset,
strand,
frame,
genePrefix,
geneNum);
} else // now in intergenic region
{
boolean write = true;
if (inPlusExon) // was in gene at previous nucleotide
{
strand = "+";
exonEnd = i;
if (firstExon) {
if (exonEnd - exonStart + 1 < 3) {
System.err.println(
"Single '"
+ strand
+ "' strand exon is < 3 bases for sequence '"
+ seqName
+ "'. exonStart="
+ exonStart
+ " exonEnd="
+ exonEnd);
write = false;
} else {
writeGFTLine(
fout,
seqName,
"start_codon",
exonStart + offset,
exonStart + offset + 2,
strand,
frame,
genePrefix,
geneNum);
}
} else if (startCodonSplit) { // at second exon that contains part of start codon
Assert.a(frame == 1 || frame == 2);
writeGFTLine(
fout,
seqName,
"start_codon",
exonStart + offset,
exonStart + offset + frame - 1,
strand,
frame,
genePrefix,
geneNum);
}
if (write) {
writeGFTLine(
fout,
seqName,
"CDS",
exonStart + offset,
exonEnd + offset,
strand,
frame,
genePrefix,
geneNum);
writeGFTLine(
fout,
seqName,
"stop_codon",
exonEnd + offset + 1,
exonEnd + offset + 3,
strand,
0,
genePrefix,
geneNum);
}
inPlusExon = false;
firstExon = true;
startCodonSplit = false;
geneNum++;
} else if (inMinusExon) {
strand = "-";
long prevExonEnd = exonEnd;
exonEnd = i;
if (firstExon && exonEnd - exonStart + 1 < 3) {
System.err.println(
"Single '"
+ strand
+ "' strand exon is < 3 bases for sequence '"
+ seqName
+ "'. exonStart="
+ exonStart
+ " exonEnd="
+ exonEnd);
} else if (exonEnd - exonStart + 1
< 3) { // this exon is < 3 bases, need to split start codon
if (exonEnd - exonStart + 1 == 2) { // this exon is 2 bases
writeGFTLine(
fout,
seqName,
"start_codon",
prevExonEnd + offset,
prevExonEnd + offset,
strand,
0,
genePrefix,
geneNum);
writeGFTLine(
fout,
seqName,
"CDS",
exonStart + offset,
exonEnd + offset,
strand,
frame,
genePrefix,
geneNum);
writeGFTLine(
fout,
seqName,
"start_codon",
exonStart + offset,
exonEnd + offset,
strand,
2,
genePrefix,
geneNum);
} else if (exonEnd - exonStart + 1 == 1) { // this exon is 1 base
writeGFTLine(
fout,
seqName,
"start_codon",
prevExonEnd + offset - 1,
prevExonEnd + offset,
strand,
0,
genePrefix,
geneNum);
writeGFTLine(
fout,
seqName,
"CDS",
exonStart + offset,
exonEnd + offset,
strand,
frame,
genePrefix,
geneNum);
writeGFTLine(
fout,
seqName,
"start_codon",
exonStart + offset,
exonEnd + offset,
strand,
1,
genePrefix,
geneNum);
}
} else {
writeGFTLine(
fout,
seqName,
"CDS",
exonStart + offset,
exonEnd + offset,
strand,
frame,
genePrefix,
geneNum);
writeGFTLine(
fout,
seqName,
"start_codon",
exonEnd + offset - 2,
exonEnd + offset,
strand,
0,
genePrefix,
geneNum);
}
inMinusExon = false;
firstExon = true;
startCodonSplit = false;
geneNum++;
}
}
}
seqCount++;
}
fout.close();
}
