Executable added; instructions updated in README. config-file updated.

README.md

@@ -22,12 +22,21 @@ sh install.sh
 ```
 
 ## Usage:
+If you have MATLAB:
 See the example config file `config-comik.txt`, for an example function call from inside Matlab:
 For simulated dataset 1 provided in the folder `sample_data/simulated_dataset1`
 ```Matlab
 comik_wrapper('config-comik.txt');
 ```
 
+For those who do not have MATLAB, we provide an executable which can be run as follows:
+```
+./run_CoMIK.sh <MATLAB_Runtime_location> <config_file>
+./run_CoMIK.sh /usr/lib/matlab-9.0 config-comik.txt
+```
+where `/usr/lib/matlab-9.0` is the typical location of the MATLAB runtime on a Linux machine.
+
+
 _CoMIK_ requires two FASTA files as input -- the first FASTA file containing sequences in the positive class; the second FASTA file containing the sequences in the negative class. Other params are explained below.
 
 Values for the following parameters are required to be set:

config-comik.txt

@@ -4,9 +4,9 @@
 ## Required Input parameters
 POSITIVE_FASTA_FILE=./sample_data/simulated_dataset1/pos.fasta
 NEGATIVE_FASTA_FILE=./sample_data/simulated_dataset1/neg.fasta
-NUMBER_OF_POSITIVES=600
-NUMBER_OF_NEGATIVES=600
-TEST_INDICES=[501:600 1101:1200]
+NUMBER_OF_POSITIVES=500
+NUMBER_OF_NEGATIVES=500
+TEST_INDICES=[401:500 901:1000]
 OUTPUT_FOLDER=comik_run_simulated_dataset1
 
 ##  ODH requirements
@@ -26,6 +26,6 @@ NUMBER_OF_INNER_FOLDS=10
 NUMBER_OF_OUTER_FOLDS=5
 WHETHER_TO_PLOT_HEATMAP=No
 WHETHER_TO_VISUALIZE_WEIGHT_VECTOR=Yes
-DEBUG_LEVEL=0
+DEBUG_LEVEL=2
 DEBUG_MSG_LOCATION=runLog.txt
 COMPUTATION_VERSION=Looping

getExpansionPoints.m

@@ -35,9 +35,10 @@
 rng('default');
 logMessages(debugMsgLocation, sprintf('with K-means: \n'), debugLevel);
 if debugLevel == 2
-    [idx, expansionPoints, sumD, matrixOfDistancesFromCentres] = kmeans(X, nClusters, 'Replicates', rep, 'Display','Iter');%, 'MaxIter',1000);%Display: final
+    [idx, expansionPoints, sumD, matrixOfDistancesFromCentres] = kmeans(X, nClusters, 'Replicates', rep, 'Display','off'); 
+    % Display could be set to 'final'
 elseif debugLevel == 0
-    [idx, expansionPoints, sumD, matrixOfDistancesFromCentres] = kmeans(X, nClusters, 'Replicates', rep, 'Display','off');%, 'MaxIter',1000);
+    [idx, expansionPoints, sumD, matrixOfDistancesFromCentres] = kmeans(X, nClusters, 'Replicates', rep, 'Display','off');
 end
 logMessages(debugMsgLocation, sprintf('--- Took %.3f seconds\n',toc), debugLevel);
 

install.sh

@@ -2,4 +2,3 @@
 
 chmod +x mkl.py
 export PATH=".:$PATH"
-

readFastaSequences.m

@@ -51,7 +51,7 @@
 % Read Sequences and their FASTA legends
 fid=fopen(txt,'r');
 ofid=fopen(strcat(outputFolder, '/ommittedFastaIds.txt'), 'a'); 
-fprintf(ofid, '----%s----\n', txt);
+fprintf(ofid, '----%s---%s----\n\n', fprintf('%s',datetime('now')), txt);
 lengths = [];
 while i < givenNSeqs % feof(fid)==0
     lineRead=fgetl(fid);