Changeset 260 for trunk/benchmarking

Timestamp:

11/09/09 02:31:18 (3 years ago)

Author:

martijn

Message:

Updated ComparisonScript?, with new 1000 affy id list

Location:

trunk/benchmarking

Files:

• U133A2-randomset.txt (added)
• src/org/bridgedb/benchmarking/ComparisonScript.java (modified) (11 diffs)
• src/org/bridgedb/benchmarking/Utils.java (modified) (2 diffs)

trunk/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java

@@ -19 +19 @@
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.FileReader;
+import java.io.FileWriter;
 import java.io.IOException;
+import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -118 +121 @@
 //              private Set<Xref> refs = new HashSet<Xref>();
                 public Map<Xref, Set<Xref>> consensus;
+                int all_the_same = 0;
+                
                 private List<SingleTest> tests = new ArrayList<SingleTest>();
                 private final DataSource base;
                 private final DataSource expected;
+
+                private final File reportFile;
                 
                 List<Xref> refs;
                 
-                TestSet (DataSource base, DataSource expected)
+                TestSet (DataSource base, DataSource expected, File dest)
                 {
                         this.base = base;
                         this.expected = expected;
+                        this.reportFile = dest;
                 }
 
@@ -156 +164 @@
                                 consensus.put (ref, maxVal);
                                 
+                                // count how many times all mappers have the same result
+                                if (max == tests.size() && maxVal != null && maxVal.size() > 0) all_the_same++;
+                                
                                 // count amount of consensus per test
                                 for (SingleTest test : tests)
                                 {
-                                        if (Utils.safeEquals (consensus.get(ref), test.result.get(ref)))
-                                        {
-                                                test.consensus++;
-                                        }
+                                        if (consensus.get(ref) != null && consensus.get(ref).size() > 0)                                        
+                                                if (Utils.safeEquals (consensus.get(ref), test.result.get(ref)))
+                                                {
+                                                        test.consensus++;
+                                                }
                                 }
 
@@ -185 +197 @@
                 }
                 
-                public void reportMerged()
-                {
-                        System.out.print ("service:");
-                        for (SingleTest single : tests)
-                        {
-                                System.out.print ("\t" + single.connector.name);
-                        }
-                        System.out.println("\tconsensus");
-
-                        System.out.print ("connecting (msec):");
-                        for (SingleTest single : tests)
-                        {
-                                System.out.print ("\t" + single.deltaConnect);
-                        }
-                        System.out.println();
-
-                        System.out.print ("mapping (msec):");
-                        for (SingleTest single : tests)
-                        {
-                                System.out.print ("\t" + single.deltaMapping);
-                        }
-                        System.out.println();
-
-                        System.out.print ("success%:");
-                        for (SingleTest single : tests)
-                        {
-                                System.out.printf ("\t%2d %3.1f%%", single.success, (double)single.success / (double)single.total * 100.0);
-                        }
-                        System.out.println();
-
-                        System.out.print ("consensus:");
-                        for (SingleTest single : tests)
-                        {
-                                System.out.printf ("\t%2d %3.1f%%", single.consensus, (double)single.consensus / (double)single.total * 100.0);
-                        }
-                        System.out.println();
-
+                public void reportMerged() throws IOException
+                {
+                        System.out.println ("Writing to file:" + reportFile.getAbsolutePath()); 
+                        PrintWriter writer = new PrintWriter (new FileWriter(reportFile));
+                        writer.print ("service:");
+                        for (SingleTest single : tests)
+                        {
+                                writer.print ("\t" + single.connector.name);
+                        }
+                        writer.println("\tconsensus");
+
+                        writer.print ("connecting (msec):");
+                        for (SingleTest single : tests)
+                        {
+                                writer.print ("\t" + single.deltaConnect);
+                        }
+                        writer.println();
+
+                        writer.print ("mapping (msec):");
+                        for (SingleTest single : tests)
+                        {
+                                writer.print ("\t" + single.deltaMapping);
+                        }
+                        writer.println();
+
+                        writer.print ("success%:");
+                        for (SingleTest single : tests)
+                        {
+                                writer.printf ("\t%2d %3.1f%%", single.success, (double)single.success / (double)single.total * 100.0);
+                        }
+                        writer.println();
+
+                        writer.print ("consensus:");
+                        for (SingleTest single : tests)
+                        {
+                                writer.printf ("\t%2d %3.1f%%", single.consensus, (double)single.consensus / (double)single.success * 100.0);
+                        }
+                        writer.println();
+
+                        writer.print ("overlap:");
+                        writer.printf ("\t%2d", all_the_same);
+                        writer.println();
+                        
                         for (Xref ref : refs)
                         {
-                                System.out.print (ref);
+                                writer.print (ref);
                                 for (SingleTest single : tests)
                                 {
-                                        System.out.print ("\t");
-                                        Utils.printRefSet(single.result.get(ref));
-                                }
-                                
-                                System.out.print ("\t");
-                                Utils.printRefSet(consensus.get(ref));
-                                
-                                System.out.println();
-                        }
+                                        writer.print ("\t");
+                                        Utils.printRefSet(writer, single.result.get(ref));
+                                }
+                                
+                                writer.print ("\t");
+                                Utils.printRefSet(writer, consensus.get(ref));
+                                
+                                writer.println();
+                        }
+                        writer.close();
                 }
 
@@ -302 +321 @@
         public void run() throws IOException, ClassNotFoundException, IDMapperException
         {
+                String version = "_v1";
+                File parent = new File ("/home/martijn/Desktop");
+                
                 List<TestSet> allTests = new ArrayList<TestSet>();
                 BioDataSource.init();
@@ -319 +341 @@
 //              List<Xref> affylist_syn = readList (new File("IDMapping_X_Test.txt"), );
 
-                TestSet ensembl_hgnc = new TestSet(BioDataSource.ENSEMBL, BioDataSource.HUGO);
+                TestSet ensembl_hgnc = new TestSet(BioDataSource.ENSEMBL, BioDataSource.HUGO, new File(parent, "comparison-ens-hgnc" + version));
                 ensembl_hgnc.readList(new File("IDMapping_En_Test.txt"));
-                ensembl_hgnc.tests.add (new SingleTest(Connector.DERBY_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.HUGO)); 
+//              ensembl_hgnc.tests.add (new SingleTest(Connector.DERBY_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.HUGO)); 
                 
                 // TODO: Synergizer ensembl produces the symbol of hgnc, not the hgnc identifiers 
@@ -330 +352 @@
                                 DataSource.getByFullName("hgnc"))); 
                 ensembl_hgnc.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE, BioDataSource.ENSEMBL_HUMAN, BioDataSource.HUGO)); 
-                ensembl_hgnc.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.HUGO)); 
+//              ensembl_hgnc.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.HUGO)); 
                 ensembl_hgnc.tests.add (new SingleTest(Connector.CRONOS, BioDataSource.ENSEMBL_HUMAN, BioDataSource.HUGO)); 
 
 
-                TestSet ensembl_entrez = new TestSet(BioDataSource.ENSEMBL, BioDataSource.ENTREZ_GENE);
+                TestSet ensembl_entrez = new TestSet(BioDataSource.ENSEMBL, BioDataSource.ENTREZ_GENE, new File(parent, "comparison-ens-entrez" + version));
                 ensembl_entrez.readList(new File("IDMapping_En_Test.txt"));
-                ensembl_entrez.tests.add (new SingleTest(Connector.DERBY_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.ENTREZ_GENE)); 
+//              ensembl_entrez.readList(new File("ensembl_genes_X.txt"));
+//              ensembl_entrez.tests.add (new SingleTest(Connector.DERBY_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.ENTREZ_GENE)); 
                 ensembl_entrez.tests.add (new SingleTest(Connector.SYNERGIZER_ENSEMBL, DataSource.getByFullName("ensembl_gene_id"),
                                 DataSource.getByFullName("entrezgene")));
@@ -342 +365 @@
                                 DataSource.getByFullName("entrezgene"))); 
                 ensembl_entrez.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE, BioDataSource.ENSEMBL_HUMAN, BioDataSource.ENTREZ_GENE)); 
-                ensembl_entrez.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.ENTREZ_GENE)); 
+//              ensembl_entrez.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.ENTREZ_GENE)); 
                 ensembl_entrez.tests.add (new SingleTest(Connector.BIOMART, DataSource.getByFullName("ensembl_gene_id"),
                                 DataSource.getByFullName("entrezgene")));
@@ -348 +371 @@
                                 BioDataSource.ENSEMBL_HUMAN, BioDataSource.ENTREZ_GENE));
         
-                TestSet affy = new TestSet(BioDataSource.AFFY, BioDataSource.ENSEMBL);
-                affy.readList (new File("IDMapping_X_Test.txt"));
-                affy.tests.add (new SingleTest(Connector.DERBY_LOCAL, BioDataSource.AFFY, BioDataSource.ENSEMBL_HUMAN));
-                affy.tests.add (new SingleTest(Connector.SYNERGIZER_ENSEMBL, DataSource.getByFullName("affy_hg_u133a"),
+                TestSet affy = new TestSet(BioDataSource.AFFY, BioDataSource.ENSEMBL, new File(parent, "comparison-affy-ens" + version));
+//              affy.readList (new File("IDMapping_X_Test.txt"));
+                affy.readList (new File("U133A2-randomset.txt"));
+//              affy.tests.add (new SingleTest(Connector.DERBY_LOCAL, BioDataSource.AFFY, BioDataSource.ENSEMBL_HUMAN));
+                affy.tests.add (new SingleTest(Connector.SYNERGIZER_ENSEMBL, DataSource.getByFullName("affy_hg_u133a_2"),
                                 DataSource.getByFullName("ensembl_gene_id")));
                 // affy mapping currently not available in BridgeWebservice
-//              affy.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE, BioDataSource.AFFY, BioDataSource.ENSEMBL_HUMAN));
-                affy.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE_LOCAL, BioDataSource.AFFY, BioDataSource.ENSEMBL_HUMAN));
+                affy.tests.add (new SingleTest(Connector.BIOMART, DataSource.getByFullName("affy_hg_u133a_2"),
+                                DataSource.getByFullName("ensembl_gene_id")));
+                affy.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE, BioDataSource.AFFY, BioDataSource.ENSEMBL_HUMAN));
+//              affy.tests.add (new SingleTest(Connector.BRIDGEWEBSERVICE_LOCAL, BioDataSource.AFFY, BioDataSource.ENSEMBL_HUMAN));
                 affy.tests.add (new SingleTest(Connector.CRONOS, BioDataSource.AFFY, BioDataSource.ENSEMBL_HUMAN)); 
                 
-                TestSet bridgedb_only = new TestSet(BioDataSource.ENSEMBL, BioDataSource.ENTREZ_GENE);
+                TestSet bridgedb_only = new TestSet(BioDataSource.ENSEMBL, BioDataSource.ENTREZ_GENE, new File(parent, "comparison-bridgedb-only" + version));
                 bridgedb_only.readList(new File("IDMapping_En_Test.txt"));
                 bridgedb_only.tests.add (new SingleTest(Connector.DERBY_LOCAL, BioDataSource.ENSEMBL_HUMAN, BioDataSource.ENTREZ_GENE)); 
@@ -366 +392 @@
 
                 // comment test that you want to skip.
-                allTests.add (bridgedb_only);
-//              allTests.add (ensembl_entrez);
-//              allTests.add (affy);
-//              allTests.add (ensembl_hgnc);
+//              allTests.add (bridgedb_only);
+                allTests.add (ensembl_entrez);
+                allTests.add (affy);
+                allTests.add (ensembl_hgnc);
                 
                 for (TestSet set : allTests)
@@ -379 +405 @@
                 
                 server.stop();
+                System.out.println ("DONE");
                 
         }

trunk/benchmarking/src/org/bridgedb/benchmarking/Utils.java

@@ -1 +1 @@
 package org.bridgedb.benchmarking;
 
+import java.io.PrintWriter;
 import java.util.HashSet;
 import java.util.Set;
@@ -30 +31 @@
         }
 
-        public static void printRefSet(Set<Xref> dests)
+        public static void printRefSet(PrintWriter writer, Set<Xref> dests)
         {
                 boolean first = true;
                 if (dests != null) for (Xref dest : dests)
                 {
-                        if (!first) System.out.print (" /// ");
-                        System.out.print (dest);
+                        if (!first) writer.print (" /// ");
+                        writer.print (dest);
                         first = false;
                 }