public ArrayList<Double> mapPDScoresToAlignment(
ArrayList<Double> pdScores, Sequence seq, ArrayList<Integer> indicesOfRowsWithSumZero) {
ArrayList<Double> result = new ArrayList<Double>();
int seqLength = seq.length();
int nonGapPosition = 0;
Symbol gap = seq.getAlphabet().getGapSymbol();
for (int i = 0; i < seqLength; i++) {
double oneScore = Double.MIN_VALUE;
boolean isSumZero = false;
isSumZero = (indicesOfRowsWithSumZero.contains(i));
boolean isGap = false;
isGap =
(seq.symbolAt(i + 1)
== gap); // note: these +1 in indices are because seq starts from one and not zero!
if (isSumZero) {
oneScore = 0.0;
} else {
oneScore = pdScores.get(nonGapPosition);
nonGapPosition++;
}
result.add(oneScore);
}
return result;
} /*mapPDScoresToAlignment*/
/** @throws BioException */
private void init() throws BioException {
similars = 0;
identicals = 0;
nGapsQ = 0;
nGapsS = 0;
for (int i = 0; i < Math.min(queryEnd - queryStart, subjectEnd - subjectStart); i++) {
Symbol a = query.symbolAt(i + queryStart);
Symbol b = subject.symbolAt(i + subjectStart);
boolean gap = false;
if (a.equals(b)) {
identicals++;
}
// get score for this pair. if it is positive, they are similar...
if (a.equals(query.getAlphabet().getGapSymbol())) {
nGapsQ++;
gap = true;
}
if (b.equals(subject.getAlphabet().getGapSymbol())) {
nGapsS++;
gap = true;
}
if (!gap && subMatrix != null && subMatrix.getValueAt(a, b) > 0) {
similars++;
}
}
}
public static String toFasta(Sequence... sequences) {
StringBuilder sb = new StringBuilder();
for (Sequence sequence : sequences)
sb.append('>' + sequence.getName() + '\n' + sequence.seqString() + '\n');
return sb.toString();
}
/** {@inheritDoc} */
@Override
protected Organism getOrganism(Sequence bioJavaSequence) throws ObjectStoreException {
Annotation anno = bioJavaSequence.getAnnotation();
// description_line=sp|Q9V8R9-2|41_DROME Isoform 2 of Protein 4.1 homolog OS=Drosophila
// melanogaster GN=cora,
String header = anno.getProperty("description_line").toString();
final String regexp = "OS\\=\\w+\\s\\w+";
Pattern p = Pattern.compile(regexp);
Matcher m = p.matcher(header);
if (m.find()) {
header = m.group();
String[] bits = header.split("=");
if (bits.length != 2) {
return null;
}
Integer taxonId = getTaxonId(bits[1]);
if (taxonId == null) {
return null;
}
Organism org = organisms.get(taxonId);
if (org == null) {
org = getDirectDataLoader().createObject(Organism.class);
org.setTaxonId(taxonId);
getDirectDataLoader().store(org);
organisms.put(taxonId, org);
}
return org;
}
return null;
}
public ArrayList<Double> mapViterbiPathToAlignment(
ArrayList<String> viterbiPath, Sequence seq, ArrayList<Integer> indicesOfRowsWithSumZero) {
ArrayList<Double> result = new ArrayList<Double>();
int seqLength = seq.length();
int nonGapPosition = 0;
Symbol gap = seq.getAlphabet().getGapSymbol();
for (int i = 0; i < seqLength; i++) {
double oneScore = Double.MIN_VALUE;
boolean isSumZero = false;
isSumZero = (indicesOfRowsWithSumZero.contains(i));
boolean isGap = false;
isGap =
(seq.symbolAt(i + 1)
== gap); // note: these +1 in indices are because seq and viterbi path start from one
// and not zero!
if (isSumZero) {
oneScore = 0.0;
} else {
if (viterbiPath.get(nonGapPosition).equals("M")) {
oneScore = 0.0;
} else if (viterbiPath.get(nonGapPosition).equals("R")) {
oneScore = 2.0;
} else if (viterbiPath.get(nonGapPosition).equals("r")) {
oneScore = 2.0;
} else if (viterbiPath.get(nonGapPosition).equals("G")) {
oneScore = 2.0;
} else if (viterbiPath.get(nonGapPosition).equals("g")) {
oneScore = 2.0;
} else if (viterbiPath.get(nonGapPosition).equals("E")) {
oneScore = 1.0;
} else if (viterbiPath.get(nonGapPosition).equals("e")) {
oneScore = 1.0;
} else if (viterbiPath.get(nonGapPosition).equals("J")) {
oneScore = 1.5;
} else {
System.err.println("Unknown charecter detected as a state name!");
}
nonGapPosition++;
}
result.add(oneScore);
}
return result;
} /*mapViterbiPathToAlignment*/
/** @return */
public float getPercentGapsQuery() {
return nGapsQ / (float) query.length() * 100;
}
/** @return */
public float getPercentGapsTarget() {
return nGapsS / (float) subject.length() * 100;
}
/**
* This method provides a BLAST-like formated alignment from the given <code>String</code>s, in
* which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to
* each line. Each line contains <code>width</code> sequence characters including the gap symbols
* plus the meta information. There is one white line between two pairs of sequences.
*
* @param width the number of symbols to be displayed per line.
* @return formated String.
* @throws BioException
*/
public String formatOutput(int width) throws BioException {
int i, j;
/*
* Highlights equal symbols within the alignment, String match/missmatch
* representation
*/
StringBuilder path = new StringBuilder();
for (i = 0; i < Math.min(queryEnd - queryStart, subjectEnd - subjectStart) + 1; i++) {
Symbol a = query.symbolAt(i + queryStart);
Symbol b = subject.symbolAt(i + subjectStart);
if (!a.equals(query.getAlphabet().getGapSymbol())
&& !b.equals(subject.getAlphabet().getGapSymbol())
&& ((subMatrix.getValueAt(a, b) >= 0) || a.equals(b))) {
path.append('|');
} else {
path.append(' ');
}
}
int maxLength = path.length();
/*
* Math.max(queryEnd - queryStart, subjectEnd - subjectStart) + 1;
*/
Formatter output = new Formatter();
output.format("%n Time (ms): %s%n", time);
output.format(" Length: %d%n", maxLength);
output.format(" Score: %d%n", getScore());
output.format(" Query: %s, Length: %d%n", query.getName(), query.length() - nGapsQ);
output.format(" Sbjct: %s, Length: %d%n", subject.getName(), subject.length() - nGapsS);
output.format(
" Identities: %d/%d, i.e., %d %% (query) and %d %% (sbjct)%n",
identicals,
maxLength,
Math.round(getPercentIdentityQuery()),
Math.round(getPercentIdentitySubject()));
output.format(
" Similars: %d/%d, i.e., %d %% (query) and %d %% (sbjct)%n",
similars,
maxLength,
Math.round(getPercentSimilarityQuery()),
Math.round(getPercentSimilaritySubject()));
output.format(
" No. gaps: %d (%d %%) in query and %d (%d %%) in sbjct%n",
nGapsQ, Math.round(getPercentGapsQuery()), nGapsS, Math.round(getPercentGapsTarget()));
int queryLPos = queryStart, queryRPos, pathLPos = 0, pathRPos;
int subjectLPos = subjectStart, subjectRPos;
int ql = queryLPos - 1, qr = queryLPos - 1, qgaps;
int sl = subjectLPos - 1, sr = subjectLPos - 1, sgaps;
int widthLeft = String.valueOf(Math.max(queryStart, queryEnd)).length();
int widthRight = String.valueOf(Math.max(queryEnd, subjectEnd)).length() + 1;
// Take width of the meta information into account.
width = Math.max(width - widthLeft - widthRight - 12, 2);
for (i = 1; i <= Math.ceil((double) maxLength / width); i++) {
// Query
queryRPos =
Math.min(
queryStart + i * width - 1,
Math.min(queryEnd, subjectEnd - subjectStart + queryStart));
qgaps = 0;
for (j = queryLPos; j <= queryRPos; j++) {
if (!query.symbolAt(j).equals(query.getAlphabet().getGapSymbol())) {
qr++;
} else {
qgaps++;
}
}
if (qgaps <= queryRPos - queryLPos) {
ql++;
}
output.format("%nQuery: %" + widthLeft + "d ", ql);
output.format("%s ", query.subStr(queryLPos, queryRPos));
output.format("%-" + widthRight + "d%n", qr);
queryLPos = queryRPos + 1;
ql = qr;
// Path
pathRPos = Math.min(i * width, path.length());
output.format(
"%-" + (widthLeft + 10) + "c%s",
Character.valueOf(' '),
path.substring(pathLPos, pathRPos));
pathLPos = pathRPos;
// Sbjct
subjectRPos =
Math.min(
subjectStart + i * width - 1,
Math.min(queryEnd - queryStart + subjectStart, subjectEnd));
sgaps = 0;
for (j = subjectLPos; j <= subjectRPos; j++) {
if (!subject.symbolAt(j).equals(subject.getAlphabet().getGapSymbol())) {
sr++;
} else {
sgaps++;
}
}
if (sgaps <= subjectRPos - subjectLPos) {
sl++;
}
output.format("%nSbjct: %" + widthLeft + "d ", sl);
output.format("%s ", subject.subStr(subjectLPos, subjectRPos));
output.format("%-" + widthRight + "d%n", sr);
subjectLPos = subjectRPos + 1;
sl = sr;
}
return output.toString();
}
/** @return */
public int getSubjectLength() {
return subject.length();
}
/** @return */
public int getQueryLength() {
return query.length();
}
/** @return */
public float getPercentIdentitySubject() {
return identicals / (float) (subject.length() - nGapsS) * 100;
}
/** @return */
public float getPercentIdentityQuery() {
return identicals / (float) (query.length() - nGapsQ) * 100;
}
/**
* @param query
* @param subject
* @param subMatrix
* @throws IllegalArgumentException
* @throws BioException
*/
public AlignmentPair(Sequence query, Sequence subject, SubstitutionMatrix subMatrix)
throws IllegalArgumentException, BioException {
this(query, subject, 1, query.length(), 1, subject.length(), subMatrix);
}
private void dnaCommand(HttpServletRequest req, DazzleResponse resp, DazzleDataSource dds)
throws IOException, DataSourceException, ServletException, DazzleException {
DazzleReferenceSource drs = (DazzleReferenceSource) dds;
List segments = DazzleTools.getSegments(dds, req, resp);
if (segments.size() == 0) {
throw new DazzleException(
DASStatus.STATUS_BAD_COMMAND_ARGUMENTS, "No segments specified for dna command");
}
// Fetch and validate the requests.
Map segmentResults = new HashMap();
for (Iterator i = segments.iterator(); i.hasNext(); ) {
Segment seg = (Segment) i.next();
try {
Sequence seq = drs.getSequence(seg.getReference());
if (seq.getAlphabet() != DNATools.getDNA()) {
throw new DazzleException(
DASStatus.STATUS_SERVER_ERROR,
"Sequence " + seg.toString() + " is not in the DNA alphabet");
}
if (seg.isBounded()) {
if (seg.getMin() < 1 || seg.getMax() > seq.length()) {
throw new DazzleException(
DASStatus.STATUS_BAD_COORDS,
"Segment " + seg.toString() + " doesn't fit sequence of length " + seq.length());
}
}
segmentResults.put(seg, seq);
} catch (NoSuchElementException ex) {
throw new DazzleException(DASStatus.STATUS_BAD_REFERENCE, ex);
} catch (DataSourceException ex) {
throw new DazzleException(DASStatus.STATUS_SERVER_ERROR, ex);
}
}
//
// Looks okay -- generate the response document
//
XMLWriter xw = resp.startDasXML("DASDNA", "dasdna.dtd");
try {
xw.openTag("DASDNA");
for (Iterator i = segmentResults.entrySet().iterator(); i.hasNext(); ) {
Map.Entry me = (Map.Entry) i.next();
Segment seg = (Segment) me.getKey();
Sequence seq = (Sequence) me.getValue();
xw.openTag("SEQUENCE");
xw.attribute("id", seg.getReference());
xw.attribute("version", drs.getLandmarkVersion(seg.getReference()));
if (seg.isBounded()) {
xw.attribute("start", "" + seg.getStart());
xw.attribute("stop", "" + seg.getStop());
} else {
xw.attribute("start", "" + 1);
xw.attribute("stop", "" + seq.length());
}
SymbolList syms = seq;
if (seg.isBounded()) {
syms = syms.subList(seg.getMin(), seg.getMax());
}
if (seg.isInverted()) {
syms = DNATools.reverseComplement(syms);
}
xw.openTag("DNA");
xw.attribute("length", "" + syms.length());
for (int pos = 1; pos <= syms.length(); pos += 60) {
int maxPos = Math.min(syms.length(), pos + 59);
xw.println(syms.subStr(pos, maxPos));
}
xw.closeTag("DNA");
xw.closeTag("SEQUENCE");
}
xw.closeTag("DASDNA");
xw.close();
} catch (Exception ex) {
throw new DazzleException(ex, "Error writing DNA document");
}
}
public void main(String[] args) throws BioException, IOException {
if (count.length != args.length) {
System.err.println("The number of counts and output file arguments does not match!");
System.exit(1);
}
OutputStream[] outputStreams;
if ((args != null) && (args.length > 0)) {
outputStreams = new OutputStream[args.length];
for (int i = 0; i < args.length; i++) {
outputStreams[i] = new BufferedOutputStream(new FileOutputStream(args[i]));
}
} else {
outputStreams = new OutputStream[] {System.out};
}
RichSequenceIterator seqIterator =
RichSequence.IOTools.readFastaDNA(new BufferedReader(new FileReader(seqFile)), null);
List<Sequence> seqs = new ArrayList<Sequence>();
while (seqIterator.hasNext()) {
seqs.add(seqIterator.nextSequence());
}
List<List<Sequence>> chosenSeqs = new ArrayList<List<Sequence>>();
if (!sampleWithReplacement) {
for (int c : count) {
List<Sequence> cseqs = new ArrayList<Sequence>();
chosenSeqs.add(cseqs);
while (c > 0) {
int randSeqIndex = random.nextInt(seqs.size());
cseqs.add(seqs.remove(randSeqIndex));
c--;
}
}
} else if (sampleWithReplacement || (length > 0)) {
/*
* if you want to sample from sequences with replacement
* or if the wanted length is specified
*/
for (int c : count) {
int i = 0;
List<Sequence> cseqs = new ArrayList<Sequence>();
chosenSeqs.add(cseqs);
while (c > 0) {
Sequence randomSeq = seqs.get(random.nextInt(seqs.size()));
if (length > 0) {
int startPos = random.nextInt(1 + randomSeq.length() - length);
cseqs.add(
new SimpleSequence(
randomSeq.subList(startPos, startPos + length),
null,
randomSeq.getName() + "_" + i++,
Annotation.EMPTY_ANNOTATION));
} else {
cseqs.add(randomSeq);
}
c--;
}
}
}
int i = 0;
for (List<Sequence> seqList : chosenSeqs) {
for (Sequence seq : seqList) {
Sequence s;
if (uniqueNames) {
s =
new SimpleSequence(
seq.subList(1, seq.length()),
null,
seq.getName() + "_" + i,
Annotation.EMPTY_ANNOTATION);
} else {
s = seq;
}
RichSequence.IOTools.writeFasta(outputStreams[i], s, null);
outputStreams[i].flush();
}
i++;
}
seqs = null;
}
/**
* Creates the Map required by the super class.
*
* @param s1
* @param s2
* @return
*/
private static Map<String, SymbolList> createHashMap(Sequence s1, Sequence s2) {
Map<String, SymbolList> m = new HashMap<String, SymbolList>();
m.put(s1.getName(), s1);
m.put(s2.getName(), s2);
return m;
}
public LinkedHashMap<SimpleAlphabet, SimpleSymbolList> getAlphabetAndSimpleSymbolList(
Matrix2D m, Sequence sequence) throws IllegalSymbolException {
LinkedHashMap<SimpleAlphabet, SimpleSymbolList> alphabetAndSymbolList =
new LinkedHashMap<SimpleAlphabet, SimpleSymbolList>();
SimpleAlphabet alphabet = new SimpleAlphabet();
List<AtomicSymbol> listOfSymbols = new ArrayList<AtomicSymbol>();
alphabet.setName("ObservedSequenceAlphabet");
int numberofRows = m.rows();
int seqLength = sequence.length();
if (numberofRows != seqLength) {
System.err.print(
"It was assumed your sequence has a length equal to the number of rows of the matrix, but found a case that is not true!");
}
Symbol gap = sequence.getAlphabet().getGapSymbol();
for (int i = 0; i < numberofRows; i++) {
List<Symbol> oneListOfSymbol = new ArrayList<Symbol>(3);
// red is match, green is flanking and blue is background
double redValue = m.get(i, 0);
double greenValue = m.get(i, 1);
double blueValue = m.get(i, 2);
double onesum = redValue + greenValue + blueValue;
boolean isGap = false;
isGap = (sequence.symbolAt(i + 1) == gap);
if (onesum
== 0) { // sum of this value is supposed to be one, but for some rows it sums up to
// zero, this is to ignore those up to time we found out why these naouthy rows
// sums up to zero!
// continue;
// note these three lines is only a dummy solution for positions where red, green and blue
// are summed up to zero!
redValue = 0.3333;
greenValue = 0.3333;
blueValue = 1 - (redValue + greenValue);
}
// make one triplet symbol from three symbols
Symbol redSymbol = AlphabetManager.createSymbol(Double.toString(redValue));
Symbol greenSymol = AlphabetManager.createSymbol(Double.toString(greenValue));
Symbol blueSymbol = AlphabetManager.createSymbol(Double.toString(blueValue));
oneListOfSymbol.add(redSymbol);
oneListOfSymbol.add(greenSymol);
oneListOfSymbol.add(blueSymbol);
// now create symbol and add it to alphabet
AtomicSymbol oneSym =
(AtomicSymbol)
AlphabetManager.createSymbol(
Annotation.EMPTY_ANNOTATION, oneListOfSymbol, alphabet);
alphabet.addSymbol(oneSym);
listOfSymbols.add(oneSym);
}
SimpleSymbolList ssl = new SimpleSymbolList(alphabet, listOfSymbols);
alphabetAndSymbolList.put(alphabet, ssl);
return alphabetAndSymbolList;
} /*getAlphabetAndSimpleSymbolList*/
/** @return */
public float getPercentSimilarityQuery() {
return similars / (float) query.length() * 100;
}
/** @return */
public float getPercentSimilaritySubject() {
return similars / (float) subject.length() * 100;
}
public void doMain(String[] args) throws Exception {
CmdLineParser parser = new CmdLineParser(this);
// if you have a wider console, you could increase the value;
// here 80 is also the default
parser.setUsageWidth(80);
try {
parser.parseArgument(args);
if ((arguments.size() != 0)) {
System.err.println(C_USAGE);
parser.printUsage(System.err);
System.exit(1);
}
if ((outPrefix == null)) {
System.err.println("Must specify outPrefix and at least one mnasePrefix");
parser.printUsage(System.err);
System.err.println(C_USAGE);
System.exit(1);
}
} catch (CmdLineException e) {
System.err.println(e.getMessage());
System.err.println(C_USAGE);
// print the list of available options
parser.printUsage(System.err);
System.err.println();
return;
}
Logger.getLogger(Logger.GLOBAL_LOGGER_NAME).setLevel(Level.SEVERE);
// Setup output files and print domain finders
ListUtils.setDelim("-");
String mnasePrefixStr = mnasePrefix;
String normString =
(this.normalizationWindow == 0)
? ""
: String.format(".normalized%dbpWind", this.normalizationWindow);
String motifString =
(this.motif == null) ? "" : String.format(".motif%s", this.motif.toUpperCase());
String withinStr =
(this.withinFeat == null) ? "" : String.format(".withinFeat-%s", this.withinFeat);
if (this.filterByMotif != null)
motifString +=
String.format(
".filteredByMotif%s%s%s",
this.filterByMotif,
(this.filterByMotifInvert) ? "-inverted" : "",
(this.filterByMotifOffset != 0)
? String.format("-offset%d", this.filterByMotifOffset)
: "");
String fwOnlyStr = (this.fwStrandOnly) ? ".fwStrandOnly" : "";
String name =
String.format(
"nucleosomeReads.%s%s%s.minReads%.2f%s.nuc%d.assoc%d%s.%s.%s",
this.outPrefix,
motifString,
withinStr,
this.minReadsPerBp,
fwOnlyStr,
this.footprintSize,
this.assocSize,
normString,
mnasePrefixStr,
methPrefix);
String outFn =
String.format(
"%s%s%s.minReads%.2f%s.nuc%d.assoc%d%s.%s.%s.csv",
this.outPrefix,
motifString,
withinStr,
this.minReadsPerBp,
fwOnlyStr,
this.footprintSize,
this.assocSize,
normString,
mnasePrefixStr,
methPrefix);
String outFnWig = outFn.replace(".csv", ".wig");
// PrintWriter pw = new PrintWriter(new FileOutputStream(outFn));
PrintWriter pwWig = new PrintWriter(new FileOutputStream(outFnWig));
// pw.printf("%s,%s\n","Meth", "ReadsPerBp");
pwWig.printf("track type=wiggle_0 name=\"%s\" description=\"%s\"\n", name, name);
MethylDbQuerier params = new MethylDbQuerier();
params.setMinCTreads(this.minCTreads);
params.setUseNonconversionFilter(!this.noNonconvFilter);
params.setMaxOppstrandAfrac(this.maxOppStrandAfrac);
params.setMaxNextNonGfrac(this.maxNextNonGfrac);
if (this.withinFeat != null) params.addFeatFilter(this.withinFeat, this.featFlank);
// We use the control table simply to limit the valid Cpg. This is a result of
// our incorrect loading of Lister 2009 tables, which contains many Cpgs which
// incorrectly yield a meth level of 0 at CpGs not covered in their sequencing data.
// This was an artifact of the way they published their data, where they published
// a list of methy-C positions without positions containing 0 mC reads, so we had
// to add fake positions for all Cs in the genome, and we didn't know which ones
// actually had coverage in their data.
List<String> methTables = Arrays.asList(methPrefix, controlMethPrefix);
// List<String> mnaseTables = Arrays.asList(mnasePrefix);
int nSeries = 1;
boolean useChipseq[] = new boolean[nSeries];
for (int i = 0; i < nSeries; i++) {
// Wow talk about a special case.
useChipseq[i] = !mnasePrefix.contains("mnase") && !mnasePrefix.contains("Schones");
}
double[] methCounts = new double[METHCOUNTER_LEN];
double[] methTotals = new double[METHCOUNTER_LEN];
int chromNum = 1;
for (String chr :
Arrays.asList(
"chr22")) // MethylDbUtils.CHROMS_MINUS_TWELVE) //MethylDbUtils.SMALL_CHROMS) //
// Arrays.asList("chr22")) //,"chr18","chr19","chr20")) //
{
System.err.printf("On chrom %d (%s)\n", chromNum++, chr);
String s = String.format("variableStep\tchrom=%s\n", chr);
pwWig.append(s);
int chrInt = (new ChromFeatures()).chrom_from_public_str(chr);
// Iterator uses DB connection and can use a ton of memory because
// it loads all rows at once. This stuff should really be added to iterator
// class, but until it is , just iterate here over the chromosome
int onCpg = 0;
// Get the full array
try {
{
ChromScoresFast counts[] = new ChromScoresFast[2];
ChromScoresFast meths[] = new ChromScoresFast[2];
int offs = 0; // 20000000; //0;
int offe = 30000000; // 0;
System.err.printf("offs=%d, offe=%d\n", offs, offe);
// The mnase counts are the same for both cases
counts =
MethylDbUtils.chromScoresReadCounts(
params, chr, this.mnasePrefix, this.refGenome, offs, offe);
// We can filter counts by a particular motif
if (this.filterByMotif != null) {
ChromScoresFast filterByMotifCounts[] = new ChromScoresFast[2];
filterByMotifCounts =
MethylDbUtils.chromScoresMotifCounts(
chr, this.refGenome, this.filterByMotif, offs, offe, false);
System.err.printf(
"%s, filtering + strand for motif %s. Pre-filter count: %.0f\n",
chr, this.filterByMotif, counts[0].getScoresTotal(chr));
counts[0].mask(filterByMotifCounts[0], this.filterByMotifInvert);
// counts[0].mask(filterByMotifCounts[1],this.filterByMotifInvert);
System.err.printf(
"%s, filtering + strand for motif %s. Post-filter count: %.0f\n",
chr, this.filterByMotif, counts[0].getScoresTotal(chr));
System.err.printf(
"%s, filtering - strand for motif %s. Pre-filter count: %.0f\n",
chr, this.filterByMotif, counts[1].getScoresTotal(chr));
counts[1].mask(filterByMotifCounts[1], this.filterByMotifInvert);
// counts[1].mask(filterByMotifCounts[0],this.filterByMotifInvert);
System.err.printf(
"%s, filtering - strand for motif %s. Post-filter count: %.0f\n",
chr, this.filterByMotif, counts[1].getScoresTotal(chr));
}
// The meth differ if it's a motif
if (this.autoMnase || this.autoMnaseFw || this.autoMnaseRev) {
meths = counts;
} else if (this.motif == null) {
meths =
MethylDbUtils.chromScoresMethLevels(
params, chr, this.methPrefix, this.refGenome, offs, offe);
} else {
char[] seqArr = null;
{
Sequence seq = GoldAssembly.chromSeq(this.refGenome, chr);
String seqStr = seq.seqString();
if (offe > 0) {
seqStr = seqStr.substring(offs, offe);
}
seqArr = seqStr.toUpperCase().toCharArray();
}
System.err.println("Seq length=" + seqArr.length);
ChromScoresMotifPositions all = new ChromScoresMotifPositions(this.refGenome);
System.err.printf(
"About to populate both strands for %s for motif %s\n", chr, this.motif);
StrandedFeature.Strand motifStrand =
(this.fwStrandOnly) ? StrandedFeature.POSITIVE : StrandedFeature.UNKNOWN;
all.populate(chr, this.motif, seqArr, offs, motifStrand);
meths[0] = all;
meths[1] = all;
// System.err.printf("Fw score at %d = %d\n",24009253,counts[0].getScore(chr,
// 24009253));
// WigOptions wo = new WigOptions();
// wo.f_step = 1;
// //counts[0] = counts[0].smooth(50, 30);
// counts[0].wigOutput("testFw.wig", wo);
// counts[1].wigOutput("testRev.wig", wo);
}
int minPos = counts[0].chromMinPos(chr);
System.err.println("Getting min pos: " + minPos);
int maxPos = counts[0].chromMaxPos(chr);
System.err.println("Getting max pos: " + maxPos);
for (int pos = minPos; pos < maxPos; pos += 1) // this.step)
{
boolean fwRead = (counts[0].getScore(chr, pos).intValue() >= 1);
boolean revRead = (counts[1].getScore(chr, pos).intValue() >= 1);
if (this.fwStrandOnly) revRead = false; // fwRead=false;
boolean enoughReads = true;
MnaseOutput mnaseReads = new MnaseOutput();
mnaseReads.rawCounts = (fwRead) ? 1 : 0;
if (this.minReadsPerBp > 0.0) {
if (fwRead) {
int nucCenter = pos + ((this.PERIODICITY - this.assocSize) / 2);
mnaseReads =
this.countMnaseReads(chr, nucCenter, counts[0], counts[1], useChipseq[0]);
} else if (revRead) {
int nucCenter = pos - ((this.PERIODICITY - this.assocSize) / 2);
mnaseReads =
this.countMnaseReads(chr, nucCenter, counts[0], counts[1], useChipseq[0]);
}
enoughReads = (mnaseReads.val >= this.minReadsPerBp);
}
// if (mnaseReads.rawCounts>2) System.err.printf("Raw counts=%d\n",
// (int)mnaseReads.rawCounts);
// enoughReads = true;
if (enoughReads && fwRead)
incrementMethCounts(chr, pos, false, methCounts, methTotals, meths, maxPos);
if (enoughReads && revRead)
incrementMethCounts(chr, pos, true, methCounts, methTotals, meths, maxPos);
//
if ((pos % 1E6) == 0)
System.err.printf("On pos #%d, meth=%d\n", pos, (int) mnaseReads.rawCounts);
if (enoughReads) {
// pwWig.printf("%d\t%.2f\n",pos, mnaseReads.val);
//// pwWig.printf("%d\t%.2f\t%.2f\t%s\n",pos,mnaseReads.rawCounts,
// mnaseReads.val, fwRead?"+":"-");
//
//// pw.printf("%d,%d", chrInt, pos);
////// pw.printf(",%.3f", mnaseReads.val);
//// pw.printf(",%d", (int)mnaseReads.rawCounts);
////// pw.printf(",%.3f", mnaseReads.normWindCount);
//// pw.println();
}
}
// Try to get rid of objects
counts[0] = null;
counts[1] = null;
meths[0] = null;
meths[1] = null;
System.gc();
}
} catch (Exception e) {
System.err.printf("%s\nCouldn't do region %s\n", e.toString(), chr);
e.printStackTrace();
}
}
// pw.close();
pwWig.close();
outFn = outFn.replace(".csv", ".methAlign.csv");
PrintWriter pw = new PrintWriter(new FileOutputStream(outFn));
ListUtils.setDelim(",");
pw.println(ListUtils.excelLine(methCounts));
pw.println(ListUtils.excelLine(methTotals));
pw.close();
} // Main
