comik_wrapper.m

function [] = comik_wrapper(configFile)

% COMIK_WRAPPER
% Usage:
%     comik_wrapper(configFile)
% 
% INPUT PARAMS
% Param 'configFile'
% Config filename with the param values set. More information on the params 
% given below
%
% Only the following params have default values:
%
% param_name			default_val
% ----------			-----------
% mklNorm			2.0
% nFolds			10
% nOuterFolds			5
% whetherToPlotHeatmap		'No'
% whetherToVisualizeWVector	'Yes'
% debugLevel			2
% debugMsgLocation		1
% computationVersion		'Looping'
% 
% Rest, params that are required to be specified:
% -----------------------------------------------
% Param 'givenFastFilename' (string)
% The input FASTA file should contain all sequences together, positives 
% followed by negatives.
%
% Params 'nPosSequences' and 'nNegSequences'
% Used to specify the number of positive and negative sequences in the dataset.
%
% Param 'testIndices' (vector)
% Indices of the sequences in the FASTA file which are to be considered as unseen 
% test examples. For example, with a FASTA file containing a total of 100 
% positive sequences followed by 100 negative sequences, the test indices 
% are given as
%       testIndices = [81:100 181:200]
% for the corresponding 20 positives and 20 negatives to be treated as test 
% examples.
% 
% Param 'outputFolder' (string)
% Specifies the path on disk where output can be written
% 
% Params 'oligoLen' and 'maxDist'
% Specify the oligomer length and the maximum distance for the ODH 
% representation. Caution: A combination of large values can be memory intensive!
%
% Param 'segmentSizeInBps'
% Specify the segment-size in basepairs for CoMIK
% 
% Param 'nClusterVals'
% Specify the number of clusters for CoMIK
%
% Param 'sigmaVals'
% Specify the sigma values for the Gaussian transformation
% 
% Param 'Cs'
% Cost values for SVM
% 
% ADDITIONAL NOTES
%
% 
% Author: snikumbh@mpi-inf.mpg.de

if nargin == 1
    % check, this should be the config filename
    % default name: config-comik.txt
    if ischar(configFile)
	if exist(configFile, 'file') == 2
	    fid = fopen(configFile, 'r');
	    l = fgetl(fid);
	    firstLineConfigFile = '## CoMIK CONFIG FILE';
	    if findstr(l, firstLineConfigFile) > 0
	        % configParams is a struct
	        configParams = readConfigFile(configFile);
	    end
            fclose(fid);
	else
	    eMsg = 'Given config file does not exist!';
	    error(eMsg);
	end
    else
	error('Error.\nInput must be a char, not a %s.', class(configFile));
    end
else
    error('Specify only the config filename!');
end 


if exist(configParams.outputFolder, 'dir') == 7
    %do-nothing
else
    status = mkdir(configParams.outputFolder);
end

% -- Perform different outer folds with parfor, asynchronously
% -- Use the given testIndices to know the percentages of examples used for 
% training and test

% Set seed for the random number generator
rng(21, 'twister');
posIndices = randperm(configParams.nPosSequences);
negIndices = randperm(configParams.nNegSequences);

posTestIndices = intersect(configParams.testIndices, posIndices);
negTestIndices = setdiff(configParams.testIndices, posIndices) - configParams.nPosSequences;

thisTestIndices{1} = configParams.testIndices;
for i=2:configParams.nOuterFolds
    thisPosTestIndices = circshift(posIndices, [0, (i-1)*length(posTestIndices)]);
    thisNegTestIndices = circshift(negIndices, [0, (i-1)*length(negTestIndices)]) + length(posIndices);
    thisTestIndices{i} = [thisPosTestIndices(end-(length(posTestIndices))+1:end) thisNegTestIndices(end-(length(negTestIndices))+1:end)];
end
%% Conditionally create a new pool; delete any existing pool of workers if NumWorkers is less than required, else use the same poolobj
poolobj = gcp('nocreate');
if isempty(poolobj)
    parpool('local', configParams.nOuterFolds);
else
    if poolobj.NumWorkers >= configParams.nOuterFolds
	logMessages(1, sprintf('Reusing existing parallel pool: %d out of %d workers\n', configParams.nOuterFolds, poolobj.NumWorkers), configParams.debugLevel);
    else
        logMessages(1, sprintf('Not enough workers in the existing parallel pool.\nDeleting existing pool with %d workers\n', poolobj.NumWorkers), configParams.debugLevel);
        delete(poolobj);
        parpool('local', configParams.nOuterFolds);
    end
end
parfor (i=1:configParams.nOuterFolds, configParams.nOuterFolds)
    thisFoldDirectory = strcat(configParams.outputFolder, '/outer_fold_', num2str(i));
    returnStatusVal = perform_one_outer_fold_for_comik(i, configParams.givenPosFastaFilename, configParams.givenNegFastaFilename, configParams.nPosSequences, ...
							configParams.nNegSequences, configParams.oligoLen, configParams.maxDist, configParams.segmentSizeInBps, ...
							configParams.nClusterVals, configParams.sigmaVals, configParams.Cs, configParams.mklNorm, configParams.nFolds, ...
							thisTestIndices{i}, configParams.debugLevel, thisFoldDirectory, configParams.whetherToPlotHeatmap, ...
							configParams.computationVersion, configParams.whetherToVisualizeWVector, configParams.debugMsgLocation);
    logMessages(1, sprintf('\nOuter fold %d: Status %s\n', i, returnStatusVal), configParams.debugLevel);
end
logMessages(1, sprintf('All outer folds completed!\n'), configParams.debugLevel);


end % comik_wrapper function ends

function statusVal = perform_one_outer_fold_for_comik(outerFoldID, givenPosFastaFilename, givenNegFastaFilename, nPosSequences, nNegSequences, oligoLen, maxDist, segmentSizeInBps, nClusterVals, sigmaVals, Cs, mklNorm, nFolds, testIndices, debugLevel, outputFolder, whetherToPlotHeatmap, computationVersion, whetherToVisualizeWVector, debugMsgLocation)
% Runs one outer fold for CoMIKL

% Make the outputFolder for this outer fold
if exist(outputFolder, 'dir') == 7
    %do-nothing
else
    status = mkdir(outputFolder);
end
% if debugMsgLocation is 1, it is the MATLAB command prompt, else a file which is to be closed at the end.
if debugMsgLocation ~= 1
    debugMsgLocation = fopen(strcat(outputFolder, '/', debugMsgLocation), 'w');
end 
% Write the testIndices to disk so that it is reproducible
testIndicesFilename = strcat(outputFolder, '/testIndicesOuterFold', num2str(outerFoldID), '.txt');
testFid = fopen(testIndicesFilename, 'a');
fprintf(testFid, 'testIndices for this outer fold:\n');
fclose(testFid);
if exist(testIndicesFilename, 'file') == 2
    dlmwrite(testIndicesFilename, sort(testIndices'),'-append', 'roffset', 1);
    logMessages(debugMsgLocation, sprintf('Test indices for this outer fold written to disk'), debugLevel);
end

for l=1:size(oligoLen,2)
    filenameSuffix = strcat('_segment-size', num2str(segmentSizeInBps), '_oligoLen', num2str(oligoLen(l)));
    runSummaryFilename = strcat(outputFolder, '/runSummary',  filenameSuffix, '.txt');
    fid = fopen(runSummaryFilename, 'a');

    fprintf(fid, '\n==================================================================================\n');
    logMessages(debugMsgLocation, sprintf('\n==================================================================================\n'), debugLevel);
    
    fprintf(fid, '   Conformal Multi-Instance Kernels for Handling Varying Length Sequences In A \n   Discriminative Setting\n');
    logMessages(debugMsgLocation, sprintf('   Conformal Multi-Instance Kernels for Handling Varying Length Sequences In A \n   Discriminative Setting\n'), debugLevel);
    
    fprintf(fid, '   Authors: Sarvesh Nikumbh, Peter Ebert, Nico Pfeifer\n\n');
    logMessages(debugMsgLocation, sprintf('   Authors: Sarvesh Nikumbh, Peter Ebert, Nico Pfeifer\n\n'), debugLevel);
    
    fprintf(fid, '   PosFasta: %s \n', givenPosFastaFilename);
    logMessages(debugMsgLocation, sprintf('   PosFasta: %s \n', givenPosFastaFilename), debugLevel);
    
    fprintf(fid, '   NegFasta: %s \n', givenNegFastaFilename);
    logMessages(debugMsgLocation, sprintf('   NegFasta: %s \n', givenNegFastaFilename), debugLevel);


    fprintf(fid, '   oligoLength: %d, maxDist: %d, segmentSize: %d bps \n', oligoLen(l), maxDist, segmentSizeInBps);
    logMessages(debugMsgLocation, sprintf('   oligoLength: %d, maxDist: %d, segmentSize: %d bps \n', oligoLen(l), maxDist, segmentSizeInBps), debugLevel);
    
    fprintf(fid, '   mklNorm: %.2f\n', mklNorm);
    logMessages(debugMsgLocation, sprintf('   mklNorm: %.2f\n', mklNorm), debugLevel);

    fprintf(fid, '   Outer Fold: %d\n', outerFoldID);
    logMessages(debugMsgLocation, sprintf('   Outer folds: %d\n', outerFoldID), debugLevel);
    
    fprintf(fid, '   Cross-validation folds: %d\n', nFolds);
    logMessages(debugMsgLocation, sprintf('   Cross-validation folds: %d\n', nFolds), debugLevel);
    
    fprintf(fid, '   #Clusters: %d \n', nClusterVals);
    logMessages(debugMsgLocation, sprintf('   #Clusters: %d \n', nClusterVals), debugLevel);
    
    fprintf(fid, '   Sigma for Gaussian RBF Xformation: %.3f\n', sigmaVals);
    logMessages(debugMsgLocation, sprintf('   Sigma for Gaussian RBF Xformation: %.3f\n', sigmaVals), debugLevel);
    
    fprintf(fid, '   C for SVM: %.3f\n', Cs);
    logMessages(debugMsgLocation, sprintf('   C for SVM: %.3f\n', Cs), debugLevel);

    fprintf(fid, '   Timestamp: %s\n', datestr(now));
    logMessages(debugMsgLocation, sprintf('   Timestamp: %s\n', datestr(now)), debugLevel);
    %
    logMessages(debugMsgLocation, sprintf('Using weight vector \n'), debugLevel);
    fprintf(fid, '   Using weight vector \n');
    %
    fprintf(fid, '===================================================================================\n');
    logMessages(debugMsgLocation, sprintf('===================================================================================\n'), debugLevel);
    fclose(fid);
    %
    %
    [allSeqsAsBags, allSeqsConformedSetKernel, kernelweights, thetaVals, instanceWeightsInEachBag, resultString, bestVals, test_teAUROC, test_teAUPRC, predictions] = comik_main_with_weight_vector(givenPosFastaFilename, givenNegFastaFilename, nPosSequences, nNegSequences, oligoLen(l), maxDist, segmentSizeInBps, nClusterVals, sigmaVals, Cs, mklNorm, nFolds, testIndices, debugLevel, debugMsgLocation, outputFolder, runSummaryFilename, whetherToPlotHeatmap, computationVersion, whetherToVisualizeWVector);
    fid=fopen(runSummaryFilename, 'a');
    fprintf(fid, '\n\n');
    fprintf(fid, '===== Validation results =====\n');
    fprintf(fid, 'OligoLen: %d, maxDist: %d, segment size: %d\n', oligoLen(l), maxDist, segmentSizeInBps);
    fprintf(fid, 'Validation teAUPRC: %.4f\n', test_teAUPRC);
    fprintf(fid, 'Validation teAUROC: %.4f\n', test_teAUROC);
    fprintf(fid, 'Best C: %.3f\n', bestVals.best_C);
    fprintf(fid, 'Best sigma: %.3f\n', bestVals.best_sigma);
    fprintf(fid, 'Best nClusters: %d\n', bestVals.best_nClusters);
    fprintf(fid, 'Best teAUROC: %.4f\n', bestVals.best_teAUROC);
    fprintf(fid, '====== END ======\n\n');
    fclose(fid);
end
if debugMsgLocation ~= 1
    % debugMsgLocation, a fileID is to be closed
    fclose(debugMsgLocation);
end

statusVal = 'OK';

end