public String induceRulesWithTestSet(double testSetPercent) throws DataFormatException {
SystemVariables.getInstance()
.appendToExperimentNotes("\\n* Total number of PSSM matches in positive sequences: ");
// System.out.println("Total number of PSSM matches in positive sequences: ");
ArrayList<Feature> posTrainingSet =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getPositiveRegulatoryRegions(),
positiveCutOffScore,
posATcomposition,
posCGcomposition);
SystemVariables.getInstance()
.appendToExperimentNotes("\\n* Total number of PSSM matches in negative sequences: ");
// System.out.println("Total number of PSSM matches in negative sequences: ");
ArrayList<Feature> negTrainingSet =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getNegativeRegulatoryRegions(),
negativeCutOffScore,
negATcomposition,
negCGcomposition);
IlpService formatter = new IlpService(tempIlpJobDirName);
formatter.createIlpFilesWithTestSet(
regulatoryRegionService.getPositiveRegulatoryRegions(),
regulatoryRegionService.getNegativeRegulatoryRegions(),
posTrainingSet,
negTrainingSet,
testSetPercent);
String ilpTheory = formatter.runILP();
return ilpTheory;
}
public IlpService createIlpFiles() throws DataFormatException {
ArrayList<Feature> posRegElements =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getPositiveRegulatoryRegions(),
positiveCutOffScore,
posATcomposition,
posCGcomposition);
if (posRegElements == null) {
posRegElements =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getPositiveRegulatoryRegions(),
regulatoryRegionService.getNegativeRegulatoryRegions(),
positiveCutOffScore);
}
// ***** Add statistics
addMotifMatchingStatisticsToNotes("positive");
SystemVariables.getInstance().setPosSeqRelElMatchesNum(posRegElements.size());
ArrayList<Feature> negRegElements =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getNegativeRegulatoryRegions(),
negativeCutOffScore,
negATcomposition,
negCGcomposition);
if (negRegElements == null) {
negRegElements =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getNegativeRegulatoryRegions(), null, negativeCutOffScore);
}
// ***** Add statistics
addMotifMatchingStatisticsToNotes("negative");
SystemVariables.getInstance().setNegSeqRelElMatchesNum(negRegElements.size());
/*
System.out.println("\n Number of matches of pairs of matrices in jurkat and erythroid sequences");
String[] pwmPair = new String[]{"MA0055.1", "MA0152.1"};
System.out.println(pwmPair[0] + " and " + pwmPair[1]+" :\t" +
FeaturesTools.numSequencesContainingAll(pwmPair, posRegElements) + "\t"+
FeaturesTools.numSequencesContainingAll(pwmPair, negRegElements));
System.out.println("\nDistances between Gata and Ebox for positive sequences:");
FeaturesTools.printRegElDistances("Gata", "Ebox", posRegElements);
*/
IlpService ilpService = new IlpService(tempIlpJobDirName);
ilpService.createIlpFiles(
regulatoryRegionService.getPositiveRegulatoryRegions(),
regulatoryRegionService.getNegativeRegulatoryRegions(),
posRegElements,
negRegElements);
return ilpService;
}
/* Generates regulatory regions for ILP positive examples.
* Base of the sequence is random ACGT 0.25 : 0.25 : 0.25 : 0.25 composition,
* cut-off score for finding PSSMs in model sequences is a default positive cut-off
* C.elegans pwm are planted in the base sequence at random positions.
*
* @param int number of regions to be generates
* @param String generic prefix for the name of regulatory sequence
*/
private ArrayList<Feature> generateRegulatoryRegions(int numOfRegions, String regionNamePrefix)
throws DataFormatException {
ArrayList<Feature> regRegions = new ArrayList<Feature>();
if (numOfRegions <= 0) {
return regRegions;
}
// Generate probabilities based on C.elegans data
// RegulatoryRegionService regRegionService =
// RegulatoryRegionServiceFactory.getService(RegulatoryRegionService.C_ELEGANS_DATA_SERVICE, 0,
// 0);
ArrayList<Feature> cElegansRegRegions = modelRegRegionService.getPositiveRegulatoryRegions();
if (cElegansRegRegions == null) {
throw new DataFormatException(
"SyntheticRegRegionService: Unable to retrieve C.elegans regulatory regions to generate positive sequences.");
}
File pwmDir = new File(SystemVariables.getInstance().getString("C.elegans.PWMs.dir"));
String tmpJobDir =
SystemVariables.getInstance()
.getString("temp.output.dir"); // TODO create a proper tmp job dir for experiments
PatserRegElementService regElService = new PatserRegElementService(pwmDir, tmpJobDir);
double cutOffScore = SystemVariables.getInstance().getPositivePatserCutOffScore();
double atComposition = sequenceNtProbabilities[0] + sequenceNtProbabilities[3];
double cgComposition = sequenceNtProbabilities[1] + sequenceNtProbabilities[2];
ArrayList<Feature> regElements =
regElService.getRegulatoryElements(
cElegansRegRegions, cutOffScore, atComposition, cgComposition);
ArrayList<RegulatoryElementPWM> regElementPWMs = regElService.getRegulatoryElementsPWMs();
StatAnalyser stat = new StatAnalyser(regElements);
for (int i = 0; i < numOfRegions; i++) {
String sequence =
generatePosExSequence(
stat,
regElementPWMs,
cElegansRegRegions.get(0).getSequence().length(),
cElegansRegRegions.size());
regRegions.add(new Feature(regionNamePrefix + i, "gene", null, 0, 0, sequence, 0.0));
}
return regRegions;
}
@Override
public void updateNumberOfPositiveRegRegions(int num) throws DataFormatException {
// TODO check for empty regions
// TODO test this
int deltaSeqNum = num - positiveRegRegions.size();
if (deltaSeqNum < 0) { // desired number of positive sequences is less than is available now
for (int i = 0; i > deltaSeqNum; i--) {
positiveRegRegions.remove(0);
}
} else { // desired number is more than available -> need to generate extra
ArrayList<Feature> extraSimulatedGenes =
FeaturesTools.generateSimulatedRegulatoryRegionsWithPositionalPSSMs(
deltaSeqNum,
regulatorySequenceLength,
sequenceNtProbabilities,
SystemVariables.getInstance().getPositivePatserCutOffScore(),
POSITIVE_REGION_PREFIX,
modelRegRegionService.getPositiveRegulatoryRegions(),
modelRegElService);
// generateRegulatoryRegions(deltaSeqNum, POSITIVE_REGION_PREFIX);
negativeRegRegions.addAll(extraSimulatedGenes);
}
}
private String createSequencesFile(ArrayList<Feature> regRegions) throws DataFormatException {
if (regRegions == null) {
throw new DataFormatException(
"Can not create regulatory sequences file for PATSER. No regulatory regions were supplied.");
}
if (tempPatserOutputDir == null
|| tempPatserOutputDir.isEmpty()) { // in case the constructor workaround was used
throw new DataFormatException(
"Can not create regulatory sequences file for PATSER. No temporary output directory was set.");
}
String seqFileName =
tempPatserOutputDir
+ SystemVariables.getInstance().getString("patser.tmp.seq.output.file.name")
+ System.currentTimeMillis();
BufferedWriter writer = null;
try {
writer = new BufferedWriter(new FileWriter(seqFileName));
for (Iterator<Feature> iterator = regRegions.iterator(); iterator.hasNext(); ) {
Feature gene = (Feature) iterator.next();
writer.write(gene.getId() + " \\" + gene.getSequence() + "\\\n");
}
writer.close();
} catch (IOException e) {
e.printStackTrace();
}
return seqFileName;
}
public SyntheticRegRegionService(int numOfPositiveRegRegions, int negExMultiplicationFactor)
throws DataFormatException {
modelRegRegionService = new CElegansRegRegionService(0);
File pwmDir = new File(SystemVariables.getInstance().getString("C.elegans.PWMs.dir"));
String tmpJobDir =
SystemVariables.getInstance()
.getString("temp.output.dir"); // TODO create a proper tmp job dir for experiments
modelRegElService = new PatserRegElementService(pwmDir, tmpJobDir);
if (modelRegRegionService.getPositiveRegulatoryRegions().size() > 0) {
regulatorySequenceLength =
modelRegRegionService.getPositiveRegulatoryRegions().get(0).getSequence().length();
} else {
throw new DataFormatException(
"Model regulatory regions are empty. Can not model synthetic regions based on an empty regions.");
}
// TODO: remove - just for testing
regulatorySequenceLength = 25;
negativeRegRegions =
FeaturesTools.generateSimulatedRegulatoryRegions(
negExMultiplicationFactor * numOfPositiveRegRegions,
regulatorySequenceLength,
NEGATIVE_REGION_PREFIX,
sequenceNtProbabilities);
positiveRegRegions =
FeaturesTools.generateSimulatedRegulatoryRegionsWithPositionalPSSMs(
numOfPositiveRegRegions,
regulatorySequenceLength,
sequenceNtProbabilities,
SystemVariables.getInstance().getPositivePatserCutOffScore(),
POSITIVE_REGION_PREFIX,
modelRegRegionService.getPositiveRegulatoryRegions(),
modelRegElService);
// this.generateRegulatoryRegions(numOfPositiveRegRegions, );
}
/* Note: unsound method
* Based on the statistics, collected when extracting motif matches by RegElementService,
* collects text note of motif matching statistics, which will be added to ILP file.
* This method has to be called immediately after RegElementService.getRegulatoryElements call,
* since every such call overrides the pssmMatchStatistics in RegElementService
*
* @param sequenceKind - can only be "positive" or "negative", depending on the kind of sequences
*/
private void addMotifMatchingStatisticsToNotes(String sequenceKind) throws DataFormatException {
Hashtable<String, Double> pssmMatchStats = regulatoryElementService.getPssmMatchingStatistics();
if (pssmMatchStats != null && !pssmMatchStats.isEmpty()) {
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Number of PSSM matches in " + sequenceKind + " sequences: ");
int numberOfRegions = 0;
if ("positive".equals(sequenceKind)) {
numberOfRegions = regulatoryRegionService.getPositiveRegulatoryRegions().size();
} else {
numberOfRegions = regulatoryRegionService.getNegativeRegulatoryRegions().size();
}
Enumeration<String> pssmMatchNames = pssmMatchStats.keys();
int totalNumMatches = 0;
String r_pssmNames = "";
String r_matches = "";
while (pssmMatchNames.hasMoreElements()) {
String pssmName = pssmMatchNames.nextElement();
double pssmStat = pssmMatchStats.get(pssmName);
int numMatches = (int) (pssmStat * numberOfRegions);
totalNumMatches = totalNumMatches + numMatches;
r_pssmNames = r_pssmNames + "\'" + pssmName + "\', ";
r_matches = r_matches + numMatches + ", ";
SystemVariables.getInstance()
.appendToExperimentNotes("\\n\\t" + pssmName + "\\t" + numMatches);
}
SystemVariables.getInstance()
.appendToExperimentNotes("\\n Total number of matches: " + totalNumMatches);
// System.out.println("In positive sequences: ");
// System.out.println(r_pssmNames);
// System.out.println(r_matches);
}
}
/*
* Runs ILP
*/
public String induceRules() throws DataFormatException {
IlpService ilpService = createIlpFiles();
System.out.println("== Created all ILP files. Starting to induce.");
//
// ==> the star of the show
//
ilpService.runILP();
// Overwrite temporary result html footer with the one that explains how to read a theory
String htmlFooterFileName =
tempIlpJobDirName + SystemVariables.getInstance().getString("html.footer.file.name");
FileHandling.writeFile(htmlFooterFileName, FileHandling.getHTMLResultsFooter(true, true));
return "Done";
}
public Explorer(
RegulatoryRegionService regRegionService,
RegulatoryElementService regElService,
String tempIlpJobDirName)
throws DataFormatException {
this.regulatoryRegionService = regRegionService;
this.regulatoryElementService = regElService;
this.tempIlpJobDirName = tempIlpJobDirName;
positiveCutOffScore = SystemVariables.getInstance().getPositivePatserCutOffScore();
negativeCutOffScore = SystemVariables.getInstance().getNegativePatserCutOffScore();
/////// Statistics
SystemVariables.getInstance().cleanStatistics(); // clean old;
SystemVariables.getInstance()
.setPosSeqNum(regulatoryRegionService.getPositiveRegulatoryRegions().size());
SystemVariables.getInstance()
.setNegSeqNum(regulatoryRegionService.getNegativeRegulatoryRegions().size());
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Number of positive sequences: "
+ regulatoryRegionService.getPositiveRegulatoryRegions().size());
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Number of negative sequences: "
+ regulatoryRegionService.getNegativeRegulatoryRegions().size());
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Patser cut-off score for positive sequences: " + positiveCutOffScore);
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* Patser cut-off score for negative sequences: " + negativeCutOffScore);
double[] posNtComposition =
FeaturesTools.getNucleotideComposition(
regulatoryRegionService.getPositiveRegulatoryRegions());
posATcomposition = posNtComposition[0] + posNtComposition[3];
posCGcomposition = posNtComposition[1] + posNtComposition[2];
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* A:T and C:G composition of positive sequences: "
+ posATcomposition
+ " "
+ posCGcomposition);
SystemVariables.getInstance().setPosATcomposition(posATcomposition);
SystemVariables.getInstance().setPosCGcomposition(posCGcomposition);
double[] negNtComposition =
FeaturesTools.getNucleotideComposition(
regulatoryRegionService.getNegativeRegulatoryRegions());
negATcomposition = negNtComposition[0] + negNtComposition[3];
negCGcomposition = negNtComposition[1] + negNtComposition[2];
SystemVariables.getInstance()
.appendToExperimentNotes(
"\\n* A:T and C:G composition of negative sequences: "
+ negATcomposition
+ " "
+ negCGcomposition);
SystemVariables.getInstance().setNegATcomposition(negATcomposition);
SystemVariables.getInstance().setNegCGcomposition(negCGcomposition);
}
/* Parses and saves an input stream of several PWMs. Each PWM is saved
* in separate file (for Patser)
* Expected input stream format:
* > matrixName
* A | 10 20 30
* C | 20 0 ...
*/
public static void savePwmFiles(String dirName, String pwmsStr)
throws DataFormatException, IOException {
int maxPwmNum = Integer.parseInt(SystemVariables.getInstance().getString("regEl.max.pwm.num"));
String line = null;
String pwmName = "";
int pwmLineCount = 0;
int pwmColNum = -1;
String pwmString = "";
StringTokenizer stMain = new StringTokenizer(pwmsStr, "\n\r");
int currPwmNum = 0;
while (stMain.hasMoreTokens()) {
line = stMain.nextToken();
line = line.trim();
if (!(line.matches("\\s*"))) { // ignore blank lines
if (pwmName.isEmpty()) { // expecting and annotated line
StringTokenizer st = new StringTokenizer(line, " \t");
String token = st.nextToken();
// Check for the line to start with ">" and read the first token after it. The rest of the
// line is ignored
if (!">".equals(token)) {
throw new DataFormatException(
"Supplied PSSM(s) are not in the correct format. Each PSSM should be preceded by a line starting with \"> pssm_name\"");
}
if (st.hasMoreTokens()) {
pwmName = st.nextToken().trim();
} else {
throw new DataFormatException(
"Supplied PSSM(s) are not in the correct format. PSSM name should follow \">\".");
}
} else { // expecting a pwm line
if (line.matches("[ACGT][\\t ]+\\|([\\t ]+[0-9]+)+")) {
int currColNum = line.split("[\\t ]+").length;
if (pwmColNum < 0) {
pwmColNum = currColNum;
} else {
if (currColNum != pwmColNum) {
throw new DataFormatException(
"Supplied PSSM(s) are not in the correct format. Unequal length of rows in one PSSM.");
}
}
pwmString = pwmString + line + "\n";
pwmLineCount++;
} else {
throw new DataFormatException("Supplied PSSM(s) are not in the correct format. ");
}
}
if (!pwmName.isEmpty() && pwmLineCount == 4) { // got all the info for writing a matrix
currPwmNum++;
// if (currPwmNum > maxPwmNum){
// throw new DataFormatException("Number of biological markers (PSSMs) has exceeded
// the limit of " +
// maxPwmNum + ".");
// }
BufferedWriter writer = new BufferedWriter(new FileWriter(dirName + pwmName + ".matrix"));
writer.write(pwmString);
writer.close();
pwmName = "";
pwmLineCount = 0;
pwmColNum = -1;
pwmString = "";
}
}
}
}
// TODO: faze it out - now I use Hash as above. Make sure that the score
public ArrayList<RegulatoryElementPWM> getRegulatoryElementsPWMs() throws DataFormatException {
String pwmLineRegEx1 = "[ACGTacgt][ \t]*\\|([ \t]*\\d+)+[ \t]*";
String pwmLineRegEx2 = "[ACGTacgt][ \t]*\\[([ \t]*\\d+)+[ \t]*\\][ \t]*";
ArrayList<RegulatoryElementPWM> pwms = new ArrayList<RegulatoryElementPWM>();
// *** Get file names of all matrixes
final String[] matrixFileNames = new File(matrixFilesDir).list();
if (matrixFileNames == null) {
throw new DataFormatException(
"Patser Regulatory Element Service has no PSSMs associated with it.");
}
for (int i = 0; i < matrixFileNames.length; i++) {
// Only read files with .matrix extension
if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
continue;
}
RegulatoryElementPWM currPwmObj = new RegulatoryElementPWM();
String tfbsName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
currPwmObj.setName(tfbsName);
BufferedReader bufferedReader = null;
try {
// for Mac
bufferedReader =
new BufferedReader(new FileReader(matrixFilesDir + "/" + matrixFileNames[i]));
// bufferedReader = new BufferedReader(new FileReader(matrixFilesDir + matrixFileNames[i]));
String line = null;
int[][] pwmArr = null;
int j = -1;
while (null != (line = bufferedReader.readLine())) {
if (line.matches(pwmLineRegEx1) || line.matches(pwmLineRegEx2)) {
j++;
if (j > 3)
throw new DataFormatException(
"Error parsing matrix file <"
+ tfbsName
+ ".matrix>. Unexpected line in the file. File should contain only one matrix.");
line = line.replaceAll("[ACGTacgt\\|\\[\\]]", ""); // remove everything but the numbers
StringTokenizer strTok = new StringTokenizer(line);
int lengthOfPwm = strTok.countTokens();
if (pwmArr == null) {
pwmArr = new int[lengthOfPwm][4];
}
if (lengthOfPwm != pwmArr.length)
throw new DataFormatException(
"Error parsing matrix file <" + tfbsName + ".matrix>. Matrix is unbalanced.");
int k = -1;
while (strTok.hasMoreElements()) {
k++;
String token = strTok.nextToken();
pwmArr[k][j] = Integer.parseInt(token);
}
}
}
currPwmObj.setPwm(pwmArr);
} catch (FileNotFoundException ex) {
ex.printStackTrace();
} catch (IOException ex) {
ex.printStackTrace();
} finally {
try {
if (bufferedReader != null) bufferedReader.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
pwms.add(currPwmObj);
} // matrix for
return pwms;
}
/* Reads the PSSM directory (saved in this instance) with a number of files that contain PSSMs and creates a Hashmap of
* these PSSMs keyed by name.
* - Each pwm file should have a .matrix extension. "." are permitted in the name (i.e. ma.123.my.matrix is acceptable)
* - Each file should have only one pwm in it.
* - No "> pmw.." lines accepted in a file. I.e nothing but the actual matrix should be present in a file
* - pwms can be of 2 formats: A | 1 2 3... or A [ 1 2 3]...
* - blank lines are permitted in the file
*/
private Hashtable<String, int[][]> readPssmsFromFileSystem() throws DataFormatException {
Hashtable<String, int[][]> resultPssms = new Hashtable<String, int[][]>();
String pssmLineRegEx1 = "[ACGTacgt][ \t]*\\|([ \t]*\\d+)+[ \t]*";
String pssmLineRegEx2 = "[ACGTacgt][ \t]*\\[([ \t]*\\d+)+[ \t]*\\][ \t]*";
// *** Get file names of all matrixes
final String[] matrixFileNames = new File(matrixFilesDir).list();
for (int i = 0; i < matrixFileNames.length; i++) {
// Only read files with .matrix extension
if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
continue;
}
String pssmName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
BufferedReader bufferedReader = null;
try {
// for Mac
bufferedReader =
new BufferedReader(new FileReader(matrixFilesDir + "/" + matrixFileNames[i]));
// bufferedReader = new BufferedReader(new FileReader(matrixFilesDir + matrixFileNames[i]));
String line = null;
int[][] pssmMatrix = null;
int j = -1;
while (null != (line = bufferedReader.readLine())) {
if (line.matches(pssmLineRegEx1) || line.matches(pssmLineRegEx2)) {
j++;
if (j > 3)
throw new DataFormatException(
"Error parsing matrix file <"
+ pssmName
+ ".matrix>. Unexpected line in the file. File should contain only one matrix.");
line = line.replaceAll("[ACGTacgt\\|\\[\\]]", ""); // remove everything but the numbers
StringTokenizer strTok = new StringTokenizer(line);
int lengthOfPwm = strTok.countTokens();
if (pssmMatrix == null) {
pssmMatrix = new int[lengthOfPwm][4];
}
if (lengthOfPwm != pssmMatrix.length)
throw new DataFormatException(
"Error parsing matrix file <" + pssmName + ".matrix>. Matrix is unbalanced.");
int k = -1;
while (strTok.hasMoreElements()) {
k++;
String token = strTok.nextToken();
pssmMatrix[k][j] = Integer.parseInt(token);
}
}
}
resultPssms.put(pssmName, pssmMatrix);
} catch (FileNotFoundException ex) {
ex.printStackTrace();
} catch (IOException ex) {
ex.printStackTrace();
} finally {
try {
if (bufferedReader != null) bufferedReader.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
} // matrix for
return resultPssms;
}
public class PatserRegElementService implements RegulatoryElementService {
private String patserInstallDirName =
SystemVariables.getInstance().getString("patser.install.dir");
private String matrixFilesDir;
private String tempPatserOutputDir;
private Hashtable<String, Double>
pssmMatchingStats; // keeps track of number of PSSM matches in all sequences / by # of
// sequences
private Hashtable<String, int[][]> pssms; // hashed by name
/*
* @param pwmDir name of the directory, which contains one or more pwm files
*/
public PatserRegElementService(File pwmDir, String tempJobDir) throws DataFormatException {
if (tempJobDir != null && !tempJobDir.isEmpty()) { // workaround for the web interface bean:
// to load example data we only need pwm dir to extract pwm info
this.tempPatserOutputDir = FileHandling.createTempPatserOutputDirectory(tempJobDir);
}
this.matrixFilesDir = pwmDir.getAbsolutePath(); // TODO
}
/* Parses a string with multiple PWMs and writes each pwm in an individual, Patser-approved file
* in a standard pwm directory, created inside a temporary directory specified.
*
* @param pmws String with one or more PWMs. The format of the String is:
* > pmwName
* A | 10 20 1 or A [10 20 1]
* C | 0 22 ... C [0 22 ...]
*
* @param tempJobDir name of a temporary directory for the whole Module Inducer run.
* A new directory will be created inside this directory to hold
* all the pwm files.
*/
public PatserRegElementService(String pwms, String tempJobDir)
throws DataFormatException, IOException {
this.tempPatserOutputDir = FileHandling.createTempPatserOutputDirectory(tempJobDir);
this.matrixFilesDir = FileHandling.createTempPwmDirectory(tempPatserOutputDir);
savePwmFiles(matrixFilesDir, pwms);
// matrixFilesDir = (new File(matrixFilesDir)).getAbsolutePath(); //TODO stupid windows hack
}
private String createSequencesFile(ArrayList<Feature> regRegions) throws DataFormatException {
if (regRegions == null) {
throw new DataFormatException(
"Can not create regulatory sequences file for PATSER. No regulatory regions were supplied.");
}
if (tempPatserOutputDir == null
|| tempPatserOutputDir.isEmpty()) { // in case the constructor workaround was used
throw new DataFormatException(
"Can not create regulatory sequences file for PATSER. No temporary output directory was set.");
}
String seqFileName =
tempPatserOutputDir
+ SystemVariables.getInstance().getString("patser.tmp.seq.output.file.name")
+ System.currentTimeMillis();
BufferedWriter writer = null;
try {
writer = new BufferedWriter(new FileWriter(seqFileName));
for (Iterator<Feature> iterator = regRegions.iterator(); iterator.hasNext(); ) {
Feature gene = (Feature) iterator.next();
writer.write(gene.getId() + " \\" + gene.getSequence() + "\\\n");
}
writer.close();
} catch (IOException e) {
e.printStackTrace();
}
return seqFileName;
}
/* Finds regulatory elements in regulatory sequences
* @param regRegions - list of regulatory regions in which to look for the reg. elements
* @param cutOffScore - minimum score cut off (-ls option in Patser). Matches with lower
* score will not be accepted
*/
public ArrayList<Feature> getRegulatoryElements(
ArrayList<Feature> regRegions, double cutOffScore, double atComposition, double cgComposition)
throws DataFormatException {
/* Verified:
* When Patser matches an "R" sequence (reverse complement), it reports a start position in the
* original sequence of the reverse complement of a PSSM.
*/
///// Patser parameters :
// double cutOffScore = SystemVariables.getInstance().getString("");
ArrayList<Feature> tfbsHits = new ArrayList<Feature>();
// *** Write genes into file acceptable by PATSER
final String seqFileName = createSequencesFile(regRegions);
// *** Get file names of all matrixes
final String[] matrixFileNames = new File(matrixFilesDir).list();
pssmMatchingStats = new Hashtable<String, Double>();
for (int i = 0; i < matrixFileNames.length; i++) {
// Only read files with .matrix extension
if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
continue;
}
// *** Run PATSER tool and extract tfbs info from its output
try {
Runtime rt = Runtime.getRuntime();
// Process pr = rt.exec("cmd /c dir");
// Process pr = rt.exec("pwd");
File patserDir = new File(patserInstallDirName);
Process pr;
if (System.getProperty("os.name").startsWith("Mac")) {
final String cmd =
"./patser-v3e -A a:t "
+ atComposition
+ " c:g "
+ cgComposition
+ " -b 1 -c -d1 -ls "
+ cutOffScore
+ " -p -s -m "
+ matrixFilesDir
+ "/"
+ matrixFileNames[i]
+ " -f "
+ seqFileName;
pr = rt.exec(new String[] {"/bin/sh", "-c", cmd}, null, patserDir);
// pr = rt.exec(cmd);
// pr = rt.exec( new String[] { "patser-v3e", "-A", "a:t 0.25 c:g 0.25", "-b", "1", "-c",
// "-d1", "-ls", "7", "-p", "-s", "-m", matrixFileNames[i], "-f", seqFileName } );
} else { // i.e. Windows
String patserCommand;
// Stupid windows hack
if (matrixFilesDir.endsWith("/")) {
patserCommand =
"cmd /c patser-v3e -A a:t "
+ atComposition
+ " c:g "
+ cgComposition
+ " -b 1 -c -d1 -ls "
+ cutOffScore
+ " -p -s -m \""
+ matrixFilesDir
+ matrixFileNames[i]
+ "\" -f \""
+ seqFileName
+ "\"";
} else {
patserCommand =
"cmd /c patser-v3e -A a:t "
+ atComposition
+ " c:g "
+ cgComposition
+ " -b 1 -c -d1 -ls "
+ cutOffScore
+ " -p -s -m \""
+ matrixFilesDir
+ "\\"
+ matrixFileNames[i]
+ "\" -f \""
+ seqFileName
+ "\"";
}
// String patserCommand = "cmd /c patser-v3e -A a:t 0.25 c:g 0.25 -b 1 -c -d1 -ls 7 -p
// -s"
// + " -m " + matrixFilesDir + matrixFileNames[i] + " -f " + seqFileName;
pr = rt.exec(patserCommand, new String[] {"PATH=C:/cygwin/bin"}, patserDir);
}
BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));
String line = null;
String pssmName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
int hits = 0;
String lastGeneName = "";
// TODO
String word;
// Read the input and filter out matrix hits data
while ((line = input.readLine()) != null) {
// System.out.println(line);
if (line.contains("position=") && line.contains("score=")) { // result line
Feature regElement = new Feature("TF_binding_site");
// Set tfbs name, but filter the .matrix extension
regElement.setName(pssmName);
// hit.setNameAttribute(matrixFileNames[i]);
StringTokenizer st = new StringTokenizer(line);
// first one is the name
word = st.nextToken();
regElement.setParent(word);
while (st.hasMoreTokens()) {
word = st.nextToken();
if (word.equals("position=")) {
word = st.nextToken();
if (word.endsWith("C")) {
regElement.setStrand("R");
word = word.substring(0, word.indexOf("C"));
} else {
regElement.setStrand("D");
}
regElement.setStartPosition(Integer.parseInt(word));
} else if (word.equals("score=")) {
word = st.nextToken();
regElement.setScore(Double.parseDouble(word));
} else if (word.equals("sequence=")) {
word = st.nextToken();
regElement.setSequence(word);
// Now that we have TFBS sequence, we can set the end position of TFBS:
regElement.setEndPosition(regElement.getStartPosition() + word.length());
}
} // end of tokenizer
// This is to calculate statistics of PSSM hits
// if (!lastGeneName.equals(regElement.getParent())){
hits++;
lastGeneName = regElement.getParent();
// }
tfbsHits.add(regElement);
}
} // end of reading patser input
pssmMatchingStats.put(pssmName, (double) hits / regRegions.size());
// int exitVal = pr.waitFor();
// System.out.println("Exited with error code " + exitVal);
} catch (IOException e) {
e.printStackTrace();
throw new DataFormatException("PATSER execution failed. ");
}
}
File seqFile = new File(seqFileName);
seqFile.delete();
/*
// add begin and end of sequence "fake" matches, or markers; like ^ and $ for begin and ed sequence in regEx
// this is for ILP to be able to induce rules with begin and end of sequence (distance, etc.)
for (Iterator<Feature> iterator = regRegions.iterator(); iterator.hasNext();) {
Feature feature = (Feature) iterator.next();
// markers are place before the sequence begins and after it ends
tfbsHits.add(new Feature("generic_marker", "begin", feature.getId(), "D", 0, 0, 0.0));
tfbsHits.add(new Feature("generic_marker", "end", feature.getId(), "D", feature.getSequence().length()+2, feature.getSequence().length()+2, 0.0));
}
*/
if (tfbsHits.isEmpty()) {
throw new DataFormatException("PATSER did not locate any motifs in the data.");
}
return tfbsHits;
}
/* Statistics for the last Patser run. With every getRegulatoryElements() run it gets overwritten.
*
* (non-Javadoc)
* @see ca.uottawa.okorol.bioinf.ModuleInducer.interfaces.RegulatoryElementService#getPssmMatchingStatistics()
*/
public Hashtable<String, Double> getPssmMatchingStatistics() {
return pssmMatchingStats;
}
/* Returns PSSMs used in this Patser instance, keyed by name
*/
public Hashtable<String, int[][]> getPssms() throws DataFormatException {
if (pssms == null || pssms.isEmpty()) {
pssms = readPssmsFromFileSystem();
}
return pssms;
}
/* Reads the PSSM directory (saved in this instance) with a number of files that contain PSSMs and creates a Hashmap of
* these PSSMs keyed by name.
* - Each pwm file should have a .matrix extension. "." are permitted in the name (i.e. ma.123.my.matrix is acceptable)
* - Each file should have only one pwm in it.
* - No "> pmw.." lines accepted in a file. I.e nothing but the actual matrix should be present in a file
* - pwms can be of 2 formats: A | 1 2 3... or A [ 1 2 3]...
* - blank lines are permitted in the file
*/
private Hashtable<String, int[][]> readPssmsFromFileSystem() throws DataFormatException {
Hashtable<String, int[][]> resultPssms = new Hashtable<String, int[][]>();
String pssmLineRegEx1 = "[ACGTacgt][ \t]*\\|([ \t]*\\d+)+[ \t]*";
String pssmLineRegEx2 = "[ACGTacgt][ \t]*\\[([ \t]*\\d+)+[ \t]*\\][ \t]*";
// *** Get file names of all matrixes
final String[] matrixFileNames = new File(matrixFilesDir).list();
for (int i = 0; i < matrixFileNames.length; i++) {
// Only read files with .matrix extension
if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
continue;
}
String pssmName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
BufferedReader bufferedReader = null;
try {
// for Mac
bufferedReader =
new BufferedReader(new FileReader(matrixFilesDir + "/" + matrixFileNames[i]));
// bufferedReader = new BufferedReader(new FileReader(matrixFilesDir + matrixFileNames[i]));
String line = null;
int[][] pssmMatrix = null;
int j = -1;
while (null != (line = bufferedReader.readLine())) {
if (line.matches(pssmLineRegEx1) || line.matches(pssmLineRegEx2)) {
j++;
if (j > 3)
throw new DataFormatException(
"Error parsing matrix file <"
+ pssmName
+ ".matrix>. Unexpected line in the file. File should contain only one matrix.");
line = line.replaceAll("[ACGTacgt\\|\\[\\]]", ""); // remove everything but the numbers
StringTokenizer strTok = new StringTokenizer(line);
int lengthOfPwm = strTok.countTokens();
if (pssmMatrix == null) {
pssmMatrix = new int[lengthOfPwm][4];
}
if (lengthOfPwm != pssmMatrix.length)
throw new DataFormatException(
"Error parsing matrix file <" + pssmName + ".matrix>. Matrix is unbalanced.");
int k = -1;
while (strTok.hasMoreElements()) {
k++;
String token = strTok.nextToken();
pssmMatrix[k][j] = Integer.parseInt(token);
}
}
}
resultPssms.put(pssmName, pssmMatrix);
} catch (FileNotFoundException ex) {
ex.printStackTrace();
} catch (IOException ex) {
ex.printStackTrace();
} finally {
try {
if (bufferedReader != null) bufferedReader.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
} // matrix for
return resultPssms;
}
/*
* (non-Javadoc)
* @see ca.uottawa.okorol.bioinf.ModuleInducer.interfaces.RegulatoryElementService#getRegulatoryElementsPWMs()
*
* Reads a directory with a number of files that contain pwms and creates an ArrayList of pwm objects.
* - Each pwm file should have a .matrix extension. "." are permitted in the name (i.e. ma.123.my.matrix is acceptable)
* - Each file should have only one pwm in it.
* - No "> pmw.." lines accepted in a file. I.e nothing but the actual matrix should be present in a file
* - pwms can be of 2 formats: A | 1 2 3... or A [ 1 2 3]...
* - blank lines are permitted in the file
* -
*/
// TODO: faze it out - now I use Hash as above. Make sure that the score
public ArrayList<RegulatoryElementPWM> getRegulatoryElementsPWMs() throws DataFormatException {
String pwmLineRegEx1 = "[ACGTacgt][ \t]*\\|([ \t]*\\d+)+[ \t]*";
String pwmLineRegEx2 = "[ACGTacgt][ \t]*\\[([ \t]*\\d+)+[ \t]*\\][ \t]*";
ArrayList<RegulatoryElementPWM> pwms = new ArrayList<RegulatoryElementPWM>();
// *** Get file names of all matrixes
final String[] matrixFileNames = new File(matrixFilesDir).list();
if (matrixFileNames == null) {
throw new DataFormatException(
"Patser Regulatory Element Service has no PSSMs associated with it.");
}
for (int i = 0; i < matrixFileNames.length; i++) {
// Only read files with .matrix extension
if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
continue;
}
RegulatoryElementPWM currPwmObj = new RegulatoryElementPWM();
String tfbsName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
currPwmObj.setName(tfbsName);
BufferedReader bufferedReader = null;
try {
// for Mac
bufferedReader =
new BufferedReader(new FileReader(matrixFilesDir + "/" + matrixFileNames[i]));
// bufferedReader = new BufferedReader(new FileReader(matrixFilesDir + matrixFileNames[i]));
String line = null;
int[][] pwmArr = null;
int j = -1;
while (null != (line = bufferedReader.readLine())) {
if (line.matches(pwmLineRegEx1) || line.matches(pwmLineRegEx2)) {
j++;
if (j > 3)
throw new DataFormatException(
"Error parsing matrix file <"
+ tfbsName
+ ".matrix>. Unexpected line in the file. File should contain only one matrix.");
line = line.replaceAll("[ACGTacgt\\|\\[\\]]", ""); // remove everything but the numbers
StringTokenizer strTok = new StringTokenizer(line);
int lengthOfPwm = strTok.countTokens();
if (pwmArr == null) {
pwmArr = new int[lengthOfPwm][4];
}
if (lengthOfPwm != pwmArr.length)
throw new DataFormatException(
"Error parsing matrix file <" + tfbsName + ".matrix>. Matrix is unbalanced.");
int k = -1;
while (strTok.hasMoreElements()) {
k++;
String token = strTok.nextToken();
pwmArr[k][j] = Integer.parseInt(token);
}
}
}
currPwmObj.setPwm(pwmArr);
} catch (FileNotFoundException ex) {
ex.printStackTrace();
} catch (IOException ex) {
ex.printStackTrace();
} finally {
try {
if (bufferedReader != null) bufferedReader.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
pwms.add(currPwmObj);
} // matrix for
return pwms;
}
/* Parses and saves an input stream of several PWMs. Each PWM is saved
* in separate file (for Patser)
* Expected input stream format:
* > matrixName
* A | 10 20 30
* C | 20 0 ...
*/
public static void savePwmFiles(String dirName, String pwmsStr)
throws DataFormatException, IOException {
int maxPwmNum = Integer.parseInt(SystemVariables.getInstance().getString("regEl.max.pwm.num"));
String line = null;
String pwmName = "";
int pwmLineCount = 0;
int pwmColNum = -1;
String pwmString = "";
StringTokenizer stMain = new StringTokenizer(pwmsStr, "\n\r");
int currPwmNum = 0;
while (stMain.hasMoreTokens()) {
line = stMain.nextToken();
line = line.trim();
if (!(line.matches("\\s*"))) { // ignore blank lines
if (pwmName.isEmpty()) { // expecting and annotated line
StringTokenizer st = new StringTokenizer(line, " \t");
String token = st.nextToken();
// Check for the line to start with ">" and read the first token after it. The rest of the
// line is ignored
if (!">".equals(token)) {
throw new DataFormatException(
"Supplied PSSM(s) are not in the correct format. Each PSSM should be preceded by a line starting with \"> pssm_name\"");
}
if (st.hasMoreTokens()) {
pwmName = st.nextToken().trim();
} else {
throw new DataFormatException(
"Supplied PSSM(s) are not in the correct format. PSSM name should follow \">\".");
}
} else { // expecting a pwm line
if (line.matches("[ACGT][\\t ]+\\|([\\t ]+[0-9]+)+")) {
int currColNum = line.split("[\\t ]+").length;
if (pwmColNum < 0) {
pwmColNum = currColNum;
} else {
if (currColNum != pwmColNum) {
throw new DataFormatException(
"Supplied PSSM(s) are not in the correct format. Unequal length of rows in one PSSM.");
}
}
pwmString = pwmString + line + "\n";
pwmLineCount++;
} else {
throw new DataFormatException("Supplied PSSM(s) are not in the correct format. ");
}
}
if (!pwmName.isEmpty() && pwmLineCount == 4) { // got all the info for writing a matrix
currPwmNum++;
// if (currPwmNum > maxPwmNum){
// throw new DataFormatException("Number of biological markers (PSSMs) has exceeded
// the limit of " +
// maxPwmNum + ".");
// }
BufferedWriter writer = new BufferedWriter(new FileWriter(dirName + pwmName + ".matrix"));
writer.write(pwmString);
writer.close();
pwmName = "";
pwmLineCount = 0;
pwmColNum = -1;
pwmString = "";
}
}
}
}
public static void savePwmFiles(String dirName, InputStream in)
throws DataFormatException, IOException {
StringBuffer out = new StringBuffer();
byte[] b = new byte[4096];
for (int n; (n = in.read(b)) != -1; ) {
out.append(new String(b, 0, n));
}
savePwmFiles(dirName, out.toString());
}
/* Phased out. Insted, convert the InputStream to a String and use a method for String
public static void savePwmFiles(String dirName, InputStream in) throws DataFormatException, IOException{
BufferedReader input = new BufferedReader(new InputStreamReader(in));
String line = null;
String pwmName = "";
int pwmLineCount = 0;
int pwmColNum = -1;
String pwmString = "";
while ((line = input.readLine()) != null) {
if (!(line.matches("\\s*"))){ //ignore blank lines
if (pwmName.isEmpty()) { // expecting and annotated line
StringTokenizer st = new StringTokenizer(line, " \t");
String token = st.nextToken();
// Check for the line to start with ">" and read the first token after it. The rest of the line is ignored
if (!">".equals(token)){
throw new DataFormatException("Supplied PSSM(s) are not in the correct format. Each PSSM should be preceded by a line starting with \"> pssm_name\"");
}
if (st.hasMoreTokens()){
pwmName = st.nextToken();
}else {
throw new DataFormatException("Supplied PSSM(s) are not in the correct format. PSSM name should follow \">\".");
}
} else { //expecting a pwm line
if (line.matches("[ACGT][\\t ]+\\|([\\t ]+[0-9]+)+")){
int currColNum = line.split("[\\t ]+").length;
if (pwmColNum < 0){
pwmColNum = currColNum;
} else {
if (currColNum != pwmColNum){
throw new DataFormatException("Supplied PSSM(s) are not in the correct format. Unequal length of rows in one PSSM.");
}
}
pwmString = pwmString + line + "\n";
pwmLineCount++;
} else {
throw new DataFormatException("Supplied PSSM(s) are not in the correct format. ");
}
}
if (!pwmName.isEmpty() && pwmLineCount == 4){ // got all the info for writing a matrix
BufferedWriter writer = new BufferedWriter(new FileWriter(dirName + pwmName + ".matrix"));
writer.write(pwmString);
writer.close();
pwmName = "";
pwmLineCount = 0;
pwmColNum = -1;
pwmString = "";
}
}
}
}
*/
/* Parses and saves an input stream of several PWMs. Each PWM is saved
* in separate file (for Patser)
* Expected input stream format:
* > matrixName
* A [ 10 20 30 ]
* C [ 20 0 ...
*
* Converted files should be of format A | 10 20 10...
*/
public static void saveAndConvertPwmFiles(String dirName, InputStream in)
throws DataFormatException, IOException {
BufferedReader input = new BufferedReader(new InputStreamReader(in));
String line = null;
String pwmName = "";
int pwmLineCount = 0;
String pwmString = "";
while ((line = input.readLine()) != null) {
if (!(line.matches("\\s*"))) { // ignore blank lines
if (pwmName.isEmpty()) { // expecting and annotated line
if (!line.startsWith(">")) {
throw new DataFormatException(
"PWM sequence is not in the correct format. Each PWM should be preceded by a line starting with \"> pwmName\"");
}
line = line.substring(1);
StringTokenizer st = new StringTokenizer(line, " \t");
if (st.hasMoreTokens()) {
pwmName = st.nextToken();
} else {
throw new DataFormatException(
"PWM sequence is not in the correct format. PWM name should follow \">\".");
}
} else { // expecting a pwm line
// if (line.matches("[ACGT][\\t ]+\\|([\\t ]+[0-9]+)+")){
line = line.replace('[', '|');
int len = line.length();
line = line.substring(0, len - 1);
pwmString = pwmString + line + "\n";
pwmLineCount++;
// } else {
// throw new DataFormatException("At least one of the PWMs is not in the correct format.
// ");
// }
}
if (!pwmName.isEmpty() && pwmLineCount == 4) { // got all the info for writing a matrix
BufferedWriter writer = new BufferedWriter(new FileWriter(dirName + pwmName + ".matrix"));
writer.write(pwmString);
writer.close();
pwmName = "";
pwmLineCount = 0;
pwmString = "";
}
}
}
}
@Override
public ArrayList<Feature> getRegulatoryElements(
ArrayList<Feature> regRegions, ArrayList<Feature> backgroundRegRegions, double cutOffScore)
throws DataFormatException {
throw new DataFormatException("This method is not applicable to Patser Service");
}
}
/* Finds regulatory elements in regulatory sequences
* @param regRegions - list of regulatory regions in which to look for the reg. elements
* @param cutOffScore - minimum score cut off (-ls option in Patser). Matches with lower
* score will not be accepted
*/
public ArrayList<Feature> getRegulatoryElements(
ArrayList<Feature> regRegions, double cutOffScore, double atComposition, double cgComposition)
throws DataFormatException {
/* Verified:
* When Patser matches an "R" sequence (reverse complement), it reports a start position in the
* original sequence of the reverse complement of a PSSM.
*/
///// Patser parameters :
// double cutOffScore = SystemVariables.getInstance().getString("");
ArrayList<Feature> tfbsHits = new ArrayList<Feature>();
// *** Write genes into file acceptable by PATSER
final String seqFileName = createSequencesFile(regRegions);
// *** Get file names of all matrixes
final String[] matrixFileNames = new File(matrixFilesDir).list();
pssmMatchingStats = new Hashtable<String, Double>();
for (int i = 0; i < matrixFileNames.length; i++) {
// Only read files with .matrix extension
if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
continue;
}
// *** Run PATSER tool and extract tfbs info from its output
try {
Runtime rt = Runtime.getRuntime();
// Process pr = rt.exec("cmd /c dir");
// Process pr = rt.exec("pwd");
File patserDir = new File(patserInstallDirName);
Process pr;
if (System.getProperty("os.name").startsWith("Mac")) {
final String cmd =
"./patser-v3e -A a:t "
+ atComposition
+ " c:g "
+ cgComposition
+ " -b 1 -c -d1 -ls "
+ cutOffScore
+ " -p -s -m "
+ matrixFilesDir
+ "/"
+ matrixFileNames[i]
+ " -f "
+ seqFileName;
pr = rt.exec(new String[] {"/bin/sh", "-c", cmd}, null, patserDir);
// pr = rt.exec(cmd);
// pr = rt.exec( new String[] { "patser-v3e", "-A", "a:t 0.25 c:g 0.25", "-b", "1", "-c",
// "-d1", "-ls", "7", "-p", "-s", "-m", matrixFileNames[i], "-f", seqFileName } );
} else { // i.e. Windows
String patserCommand;
// Stupid windows hack
if (matrixFilesDir.endsWith("/")) {
patserCommand =
"cmd /c patser-v3e -A a:t "
+ atComposition
+ " c:g "
+ cgComposition
+ " -b 1 -c -d1 -ls "
+ cutOffScore
+ " -p -s -m \""
+ matrixFilesDir
+ matrixFileNames[i]
+ "\" -f \""
+ seqFileName
+ "\"";
} else {
patserCommand =
"cmd /c patser-v3e -A a:t "
+ atComposition
+ " c:g "
+ cgComposition
+ " -b 1 -c -d1 -ls "
+ cutOffScore
+ " -p -s -m \""
+ matrixFilesDir
+ "\\"
+ matrixFileNames[i]
+ "\" -f \""
+ seqFileName
+ "\"";
}
// String patserCommand = "cmd /c patser-v3e -A a:t 0.25 c:g 0.25 -b 1 -c -d1 -ls 7 -p
// -s"
// + " -m " + matrixFilesDir + matrixFileNames[i] + " -f " + seqFileName;
pr = rt.exec(patserCommand, new String[] {"PATH=C:/cygwin/bin"}, patserDir);
}
BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));
String line = null;
String pssmName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
int hits = 0;
String lastGeneName = "";
// TODO
String word;
// Read the input and filter out matrix hits data
while ((line = input.readLine()) != null) {
// System.out.println(line);
if (line.contains("position=") && line.contains("score=")) { // result line
Feature regElement = new Feature("TF_binding_site");
// Set tfbs name, but filter the .matrix extension
regElement.setName(pssmName);
// hit.setNameAttribute(matrixFileNames[i]);
StringTokenizer st = new StringTokenizer(line);
// first one is the name
word = st.nextToken();
regElement.setParent(word);
while (st.hasMoreTokens()) {
word = st.nextToken();
if (word.equals("position=")) {
word = st.nextToken();
if (word.endsWith("C")) {
regElement.setStrand("R");
word = word.substring(0, word.indexOf("C"));
} else {
regElement.setStrand("D");
}
regElement.setStartPosition(Integer.parseInt(word));
} else if (word.equals("score=")) {
word = st.nextToken();
regElement.setScore(Double.parseDouble(word));
} else if (word.equals("sequence=")) {
word = st.nextToken();
regElement.setSequence(word);
// Now that we have TFBS sequence, we can set the end position of TFBS:
regElement.setEndPosition(regElement.getStartPosition() + word.length());
}
} // end of tokenizer
// This is to calculate statistics of PSSM hits
// if (!lastGeneName.equals(regElement.getParent())){
hits++;
lastGeneName = regElement.getParent();
// }
tfbsHits.add(regElement);
}
} // end of reading patser input
pssmMatchingStats.put(pssmName, (double) hits / regRegions.size());
// int exitVal = pr.waitFor();
// System.out.println("Exited with error code " + exitVal);
} catch (IOException e) {
e.printStackTrace();
throw new DataFormatException("PATSER execution failed. ");
}
}
File seqFile = new File(seqFileName);
seqFile.delete();
/*
// add begin and end of sequence "fake" matches, or markers; like ^ and $ for begin and ed sequence in regEx
// this is for ILP to be able to induce rules with begin and end of sequence (distance, etc.)
for (Iterator<Feature> iterator = regRegions.iterator(); iterator.hasNext();) {
Feature feature = (Feature) iterator.next();
// markers are place before the sequence begins and after it ends
tfbsHits.add(new Feature("generic_marker", "begin", feature.getId(), "D", 0, 0, 0.0));
tfbsHits.add(new Feature("generic_marker", "end", feature.getId(), "D", feature.getSequence().length()+2, feature.getSequence().length()+2, 0.0));
}
*/
if (tfbsHits.isEmpty()) {
throw new DataFormatException("PATSER did not locate any motifs in the data.");
}
return tfbsHits;
}
