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[DL-Learner SVN] SF.net SVN: dl-learner:[2598] trunk/scripts/src/main/java/org/dllearner/ examples/pdb
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From: <km...@us...> - 2011-01-11 23:04:53
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Revision: 2598
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2598&view=rev
Author: kmpf
Date: 2011-01-11 23:04:45 +0000 (Tue, 11 Jan 2011)
Log Message:
-----------
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-01-11 14:38:13 UTC (rev 2597)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-01-11 23:04:45 UTC (rev 2598)
@@ -1,11 +1,13 @@
package org.dllearner.examples.pdb;
import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
import java.io.IOException;
-import java.io.OutputStream;
+import java.io.PrintStream;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
@@ -13,9 +15,10 @@
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ResIterator;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.dumontierlab.pdb2rdf.model.PdbRdfModel;
import com.dumontierlab.pdb2rdf.parser.PdbXmlParser;
@@ -24,50 +27,57 @@
public class HelixRDFCreator {
+
+ private static ArrayList<Resource> positives;
+ private static ArrayList<Resource> negatives;
/**
* @param args
+ * TODO: remove beginsAt, endsAt from model
*/
public static void main(String[] args) {
- TrainAndTestSet sets = new TrainAndTestSet(2);
- String[] trainIDs = sets.getTrainset();
+
+
+ TrainAndTestSet sets = new TrainAndTestSet(1);
PdbRdfModel trainmodel = new PdbRdfModel();
+ trainmodel.add(getRdfModelForIds(sets.getTrainset()));
+ /*
+ * String[] id = {"200L"};
+ * trainmodel.add(getRdfModelForIds(id));
+ */
- for(int i = 0; i < trainIDs.length; i++){
- System.out.println(trainIDs[i]);
- String[] ID = {trainIDs[i]};
- trainmodel.add(getRdfModelForIds(ID));
- }
-
- getRdfModelForIds(sets.getTrainset());
// PdbRdfModel testmodel = getRdfModelForIds(sets.getTestset());
+ ResIterator niter = getFirstAA(trainmodel);
+
+ /* take all amino acids which are in helices and put them into the
+ * positives ArrayList, and all others in the negatives ArrayList
+ */
+ createPositivesAndNegatives(niter, trainmodel);
+
+ /*
+ * writes the conf-File
+ */
+ createConfFile();
+
+
try
{
- String queryString =
- "PREFIX pdb: <http://bio2rdf.org/pdb> " +
- "CONSTRUCT { ?x1 ?x2 ?x3 .} " +
- "WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> . ?x1 ?x2 ?x3 .}";
- Query query = QueryFactory.create(queryString);
+ SimpleDateFormat df = new SimpleDateFormat("_yyyy_MM_dd");
+ String filename = "Helixtrainer" + df.format(new Date()) + ".rdf";
+ PrintStream out = new PrintStream (new File(filename));
+
+ // Output query results
+ trainmodel.write(out, "RDF/XML");
- // Execute the query and obtain results
- QueryExecution qe = QueryExecutionFactory.create(query, trainmodel);
- Model construct = qe.execConstruct();
- OutputStream out = new FileOutputStream (new File("qwertzu_iop.rdf"));
- // Output query results
- construct.write(out, "RDF/XML");
-
-
-
-
- // Important - free up resources used running the query
+ // Important - free up resources used running the query
+ out.close();
}
- catch (FileNotFoundException e)
+ catch (IOException e)
{
- System.err.println("Datei nicht gefunden!");
+ System.err.println("OutputStream konnte nicht geschlossen werden!");
}
-
}
private static PdbRdfModel getRdfModelForIds(String[] pdbIDs) {
@@ -81,11 +91,10 @@
while (i.hasNext()) {
final InputSource input = i.next();
- PdbRdfModel model = new PdbRdfModel();
- model = parser.parse(input, new PdbRdfModel());
+ PdbRdfModel model = parser.parse(input, new PdbRdfModel());
// jedes Model muss gleich nach den relevanten Daten durchsucht werden,
// da ansonsten Probleme mit der Speichergröße auftreten können.
- allmodels.add(getHelices(model));
+ allmodels.add(getData(model));
}
} catch (IOException e) {
@@ -98,36 +107,156 @@
return allmodels;
}
- private static PdbRdfModel collectData (PdbRdfModel inmodel) {
- PdbRdfModel collectmodel = new PdbRdfModel();
- collectmodel.add(getHelices(inmodel));
+ private static PdbRdfModel getData(PdbRdfModel model) {
+
+ // Beispiel einer SELECT Abfrage
+ /* String selectQuery =
+ * "SELECT { ?x1 ?x2 ?x3 .} " +
+ * "WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> .}";
+ * Query query = QueryFactory.create(selectQuery);
+ * QueryExecution qe = QueryExecutionFactory.create(query, model);
+ * ResultSet select = qe.execSelect();
+ * ResultSetFormatter.out (System.out, select, query);
+ *
+ */
-
- return collectmodel;
- }
-
- private static Model getHelices(PdbRdfModel model) {
- // Zweimal dasselbe Ergebnis einmal als SELECT und einmal als CONSTRUCT (für weitere Bearbeitung) Statement
- // SELECT Abfrage
+ // CONSTRUCT Abfrage
+
+ PdbRdfModel construct = new PdbRdfModel();
String queryString =
- " SELECT ?x1 ?x2 ?x3 WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> . ?x1 ?x2 ?x3 .}";
+ /* i do it kind of difficult, but i want to be certain that i only get the sequences of
+ Polypeptides(L) which contain at least one Helix. Furthermore i collect the information
+ about at which position helices begin and end.
+ NOTE: this information has to be removed before oututing the model. But i will use this
+ to check for positive and negative train amino acids
+ */
+ "PREFIX pdb: <http://bio2rdf.org/pdb:> " +
+ "CONSTRUCT { ?x1 <http://bio2rdf.org/pdb:beginsAt> ?x2 ." +
+ " ?x1 <http://bio2rdf.org/pdb:endsAt> ?x3 . " +
+ " ?x5 <http://purl.org/dc/terms/isPartOf> ?x4 . " +
+ " ?x5 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?x6 ." +
+ " ?x5 <http://bio2rdf.org/pdb:isImmediatelyBefore> ?x7 . } " +
+ "WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> ." +
+ " ?x1 <http://bio2rdf.org/pdb:beginsAt> ?x2 ." +
+ " ?x1 <http://bio2rdf.org/pdb:endsAt> ?x3 ." +
+ " ?x3 <http://purl.org/dc/terms/isPartOf> ?x4 ." +
+ " ?x4 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Polypeptide(L)> ." +
+ " ?x5 <http://purl.org/dc/terms/isPartOf> ?x4 ." +
+ " ?x5 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?x6 ." +
+ // with the Optional clause i get the information by which amino acid
+ // a amino acid is followed
+ " OPTIONAL { ?x5 <http://bio2rdf.org/pdb:isImmediatelyBefore> ?x7 . } .}";
+
Query query = QueryFactory.create(queryString);
QueryExecution qe = QueryExecutionFactory.create(query, model);
- ResultSet select = qe.execSelect();
- ResultSetFormatter.out (System.out, select, query);
- // CONSTRUCT Abfrage
- queryString =
- "PREFIX pdb: <http://bio2rdf.org/pdb> " +
- "CONSTRUCT { ?x1 ?x2 ?x3 .} " +
- "WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> . ?x1 ?x2 ?x3 .}";
- query = QueryFactory.create(queryString);
-
- // Execute the query and obtain results
- qe = QueryExecutionFactory.create(query, model);
- Model construct = qe.execConstruct();
+ construct.add(qe.execConstruct());
qe.close();
return construct;
}
+
+ private static ResIterator getFirstAA( PdbRdfModel model) {
+ PdbRdfModel construct = new PdbRdfModel();
+ /* i search for all amino acids (AA) that have a successor
+ * but do not have a predecessor -> it's the first AA of every
+ * polypeptide chain
+ */
+
+ String queryString =
+ "PREFIX pdb: <http://bio2rdf.org/pdb:> " +
+ "CONSTRUCT { ?x1 pdb:isImmediatelyBefore ?x2 . } " +
+ "WHERE { ?x1 pdb:isImmediatelyBefore ?x2 . " +
+ // NOT EXISTS can be used with SPARQL 1.1
+ //"NOT EXISTS { ?x3 pdb:isImmediatelyBefore ?x1 . } }";
+ " OPTIONAL { ?x3 pdb:isImmediatelyBefore ?x1 . } " +
+ " FILTER ( !BOUND(?x3) ) }";
+ Query query = QueryFactory.create(queryString);
+ QueryExecution qe = QueryExecutionFactory.create(query, model);
+ construct.add(qe.execConstruct());
+ qe.close();
+ ResIterator niter = construct.listSubjects();
+ return niter;
+ }
+
+ private static void createPositivesAndNegatives(ResIterator riter, PdbRdfModel model) {
+
+ // Properties i have to use to check for while going through the AA-chain
+ Property iib = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "isImmediatelyBefore");
+ Property ba = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "beginsAt");
+ Property ea = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "endsAt");
+ ArrayList<Resource> pos = new ArrayList<Resource>();
+ ArrayList<Resource> neg = new ArrayList<Resource>();
+
+
+ // every first amino acid indicates a new AA-chain
+ while (riter.hasNext()) {
+ // Initialization of variables needed
+ Resource aaOne = riter.nextResource();
+ Resource obj = aaOne;
+ Resource nobj = aaOne;
+ boolean inHelix = false;
+
+ // look if there is a next AA
+ do {
+ // looks weird, but is needed to enter loop even for the last AA which does not have a iib-Property
+ obj = nobj;
+ // die Guten ins Töpfchen ...
+ // if we get an non-empty iterator for pdb:beginsAt the next AAs are within a AA-chain
+ if(model.listResourcesWithProperty(ba, obj).hasNext() && !inHelix ){
+ inHelix = true;
+ System.out.println("Entering Helix!");
+ }
+ // die Schlechten ins Kröpfchen
+ // if we get an non-empty iterator for pdb:endsAt and are already within a AA-chain
+ // the AAs AFTER the current ones aren't within a helix
+ if (model.listResourcesWithProperty(ea, obj).hasNext() && inHelix){
+ inHelix = false;
+ System.out.println("Leaving Helix!");
+ }
+ // get next AA if there is one
+ if (model.listObjectsOfProperty(obj, iib).hasNext()){
+ nobj = model.getProperty(obj, iib).getResource();
+ }
+
+ // do something different if we are in a helix
+ if (inHelix){
+ pos.add(obj);
+ System.out.println(obj.getURI() + " " + iib.getURI() + " " + nobj.getURI() + " we are in!");
+ } else {
+ neg.add(obj);
+ System.out.println(obj.getURI() + " " + iib.getURI() + " " + nobj.getURI());
+ }
+
+ } while (obj.hasProperty(iib)) ;
+ }
+ positives = pos;
+ negatives = neg;
+ }
+ private static void createConfFile(){
+ try
+ {
+ SimpleDateFormat df = new SimpleDateFormat("_yyyy_MM_dd");
+ String filename = "pdb" + df.format(new Date()) + ".conf";
+ PrintStream out = new PrintStream (new File(filename));
+
+ out.println("import(\"AA_properties.owl\");");
+ out.println("import(\"" + filename + "\");");
+ out.println();
+
+ for (int i = 0 ; i < positives.size() ; i++ ) {
+ out.println("+\"" + positives.get(i).getURI() + "\"");
+ }
+
+ for (int i = 0 ; i < negatives.size() ; i++ ) {
+ out.println("-\"" + negatives.get(i).getURI() + "\"");
+ }
+ // Important - free up resources used running the query
+ out.close();
+ }
+ catch (IOException e)
+ {
+ System.err.println("OutputStream konnte nicht geschlossen werden!");
+ }
+ }
}
\ No newline at end of file
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java 2011-01-11 14:38:13 UTC (rev 2597)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java 2011-01-11 23:04:45 UTC (rev 2598)
@@ -1,8 +1,5 @@
package org.dllearner.examples.pdb;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.LineNumberReader;
@@ -81,14 +78,11 @@
this.pdbprotlines = arraylist;
return count;
- } catch (FileNotFoundException e) {
+ }
+ catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return 0;
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- return 0;
}
}
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