Fixed: 1. ommittedFastaIds also prinds sequences indices; 2. comikl_m…

…ain function correct handles the adjustment of testIndices

comikl_main_with_weight_vector.m

@@ -33,26 +33,31 @@
 
 % Read positives
 logMessages(debugMsgLocation,sprintf('Positives...'), debugLevel);
-[nPos, posIndices, allSeqsRawPosFasta] = readFastaSequences(givenPosFastaFilename, chunkSizeInBps, givenNPos, outputFolder, debugLevel, debugMsgLocation);
+[nPos, ommittedPosIndices, allSeqsRawPosFasta] = readFastaSequences(givenPosFastaFilename, chunkSizeInBps, givenNPos, outputFolder, debugLevel, debugMsgLocation);
 % nPos and nNeg be could smaller than equal to givenNPos and givenNNeg resp. due to ommitting any sequences
 % whose length is less than the chunkSizeInBps
 %
 % Read Negatives
 logMessages(debugMsgLocation,sprintf('Negatives...'), debugLevel);
-[nNeg, negIndices, allSeqsRawNegFasta] = readFastaSequences(givenNegFastaFilename, chunkSizeInBps, givenNNeg, outputFolder, debugLevel, debugMsgLocation);
+[nNeg, ommittedNegIndices, allSeqsRawNegFasta] = readFastaSequences(givenNegFastaFilename, chunkSizeInBps, givenNNeg, outputFolder, debugLevel, debugMsgLocation);
 % Combine positives + negatives
 nBags = nPos + nNeg;
 % Check if we need to update the testIndices if some sequences have been ommitted
 % if posIndices and negIndices are empty, then no update required
-if ~isempty(posIndices)
-    testIndices(find(ismember(testIndices, posIndices))) = [];
+if ~isempty(ommittedPosIndices)
+    %nOmmitted = length(find(ismember(testIndices, ommittedPosIndices)));
+    testIndices(find(ismember(testIndices, ommittedPosIndices))) = [];
+    %logMessages(debugMsgLocation,sprintf('%d positive sequences ommitted from test set.\n', nOmmitted), debugLevel);
 end
-if ~isempty(negIndices)
-    testIndices(find(ismember(testIndices, nPos+negIndices))) = [];%offset by nPos
+if ~isempty(ommittedNegIndices)
+    %nOmmitted = length(find(ismember(testIndices, ommittedNegIndices)));
+    testIndices(find(ismember(testIndices, nPos+ommittedNegIndices))) = [];%offset by nPos
+    %logMessages(debugMsgLocation,sprintf('%d negative sequences ommitted from test set.\n', nOmmitted), debugLevel);
 end
-% Additionally, one needs to account for the reduction in the number of sequences affecting the indices
+% Additionally, one needs to account for the reduction in the number of sequences affecting the indices. Remove indices > nBags 
+%testIndices = testIndices(testIndices <= nBags);
 for i=1:length(testIndices)
-    testIndices(i) = testIndices(i) - nnz(posIndices < testIndices(i)) - nnz(negIndices < testIndices(i));
+    testIndices(i) = testIndices(i) - nnz(ommittedPosIndices < testIndices(i)) - nnz( (nPos+ommittedNegIndices) < testIndices(i));
 end
 % Put them together
 allSeqsRawFasta.sequence = cell(1, nBags);
@@ -64,8 +69,12 @@
     allSeqsRawFasta.sequence{i+nPos} = allSeqsRawNegFasta.sequence{i};%offset by nPos
 end
 clear allSeqsRawNegFasta;
-% Write test indices to disk for reproducibility
-dlmwrite(strcat(outputFolder, '/testIndices.txt'), testIndices);
+% Write the revised set test indices to disk for reproducibility
+
+if ~isempty(ommittedPosIndices) | ~isempty(ommittedNegIndices)
+    sortedTestIndices = sort(testIndices);
+    dlmwrite(strcat(outputFolder, '/testIndices_New.txt'), sortedTestIndices');
+end
 
 % generate labels
 % handle imbalance, multiply this to C for negatives
@@ -112,7 +121,7 @@
 nBagsForTest = nBags-idx1;
 logMessages(debugMsgLocation,sprintf('#Test: %d\n#Train: %d\n', nBagsForTest, nBagsForTrain), debugLevel);
 logMessages(debugMsgLocation,sprintf('Segmentation statistics:\n'), debugLevel);
-logMessages(debugMsgLocation,sprintf(' Mean number of instancesa in bags: %.2f\t Median: %d\t Max.: %d\t Min.: %d\n', mean(thisInstances), median(thisInstances), max(thisInstances), min(thisInstances)), debugLevel);
+logMessages(debugMsgLocation,sprintf(' Mean number of instances in bags: %.2f\t Median: %d\t Max.: %d\t Min.: %d\n', mean(thisInstances), median(thisInstances), max(thisInstances), min(thisInstances)), debugLevel);
 % Variable 'nBags' holds nBagsForTrain + nBagsForTest
 %
 % 2. Compute the instanceWide kernel that is used further
@@ -250,13 +259,13 @@
 %
 % Use the best param combinations to train using the whole trainiing set and predict the test set here
 %
-logMessages(debugMsgLocation,sprintf('---Test---\n'), debugLevel);
+logMessages(debugMsgLocation,sprintf('---Re-training and Test---\n'), debugLevel);
 % Re-train the model with all train instances together
 % trainIndicesInBags is 1:nBagsForTrain
 nClusters = bestParamComb.best_nClusters;
 conformalXformationParam = bestParamComb.best_sigma;
-logMessages(debugMsgLocation,sprintf('nClusters: %d, sigma: %d\n', nClusters, conformalXformationParam), debugLevel);
-logMessages(debugMsgLocation,sprintf('Re-training uisng complete trainning set examples...\n'), debugLevel);
+logMessages(debugMsgLocation,sprintf('Best param-values:\nSVM-Cost:%.3f, nClusters: %d, sigma: %.3f\n', nClusters, conformalXformationParam), debugLevel);
+logMessages(debugMsgLocation,sprintf('Re-training using complete trainning set examples...\n'), debugLevel);
 
 logMessages(debugMsgLocation,sprintf('Conformed Multi-instance kernel for all bags...\n'), debugLevel);
 [allSeqsConformedSetKernel, rawConformedSetKernel, allSeqsTransformationKernel, clusterCentres] = ...
@@ -364,7 +373,11 @@
     % 
     logMessages(debugMsgLocation,sprintf('Bias value: %.4f\n', biasValue), debugLevel);
     yhat = yhatTemp + biasValue;
+    if(length(Youtertest) == length(yhat))
+        logMessages(debugMsgLocation, sprintf('%d and %d: Dimensions of yhat and ytest match!\n', length(Youtertest), length(yhat)), debugLevel);
+    end
     dlmwrite(strcat(outputFolder,'/predictedLabelsWeightVector.txt'), yhat');
+    dlmwrite(strcat(outputFolder,'/givenLabels.txt'), Youtertest');
     logMessages(debugMsgLocation,sprintf('Predicted labels written to disk. Computing the auROC/auPRC, this may take some time...\n'), debugLevel);
     tic;
     [test_teAUROC, test_teAUPRC] = libsvm_plotroc(Youtertest', yhat', 'personal');

comikl_wrapper.m

@@ -357,7 +357,7 @@ case char('distal-proximal-cgi')
 fprintf(testFid, 'testIndices for this outer fold:\n');
 fclose(testFid);
 if exist(testIndicesFilename, 'file') == 2
-    dlmwrite(testIndicesFilename, testIndices','-append', 'roffset', 1);
+    dlmwrite(testIndicesFilename, sort(testIndices'),'-append', 'roffset', 1);
     logMessages(debugMsgLocation, sprintf('Test indices for this outer fold written to disk'), debugLevel);
 end
 

readFastaSequences.m

@@ -1,4 +1,4 @@
-function [nSeqs, indices, passFasta] = readFastaSequences(txt, chunkSizeInBps, givenNSeqs, outputFolder, debugLevel, debugMsgLocation)
+function [nSeqs, ommittedIndices, passFasta] = readFastaSequences(txt, chunkSizeInBps, givenNSeqs, outputFolder, debugLevel, debugMsgLocation)
 
 % FUNCTION FASTA=READFASTA(FILENAME)
 %
@@ -25,7 +25,7 @@
 fasta.legend   = cell(1, givenNSeqs);
 fasta.sequence = cell(1, givenNSeqs);
 i=0;
-indices = [];
+ommittedIndices = [];
 fasta.title=[txt,',  read: ',date];
 % READS SEQUENCES AND THEIR LEGENDS
 fid=fopen(txt,'r');
@@ -44,8 +44,8 @@
 	    if lengths(end) >= chunkSizeInBps
                 fasta.sequence{i}=[fasta.sequence{i},upper(lineRead)];
 	    else % we omit that sequence
-		indices = [indices i];
-		fprintf(ofid, fasta.legend{i});
+		ommittedIndices = [ommittedIndices i];
+		fprintf(ofid, '%d\t%s', i, fasta.legend{i});
 		fprintf(ofid, '\n');
 	    end
         end
@@ -54,7 +54,7 @@
 fclose(ofid);
 fclose(fid);
 ineligibleLengths = lengths(lengths < chunkSizeInBps);
-ineligibleIndices = find(lengths <= chunkSizeInBps);
+ineligibleIndices = find(lengths < chunkSizeInBps);
 nSeqs = givenNSeqs;
 passFasta = fasta;
 if size(ineligibleLengths, 2) > 0