From 4ca6f92ceb4b2f8c504431cf56f8a6135187a61c Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Mon, 11 Mar 2013 12:36:42 -0400
Subject: adding matlab code

---
 src/matlab/quikrCustomTrained.m | 42 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 src/matlab/quikrCustomTrained.m

(limited to 'src/matlab/quikrCustomTrained.m')

diff --git a/src/matlab/quikrCustomTrained.m b/src/matlab/quikrCustomTrained.m
new file mode 100644
index 0000000..b58aa31
--- /dev/null
+++ b/src/matlab/quikrCustomTrained.m
@@ -0,0 +1,42 @@
+function xstar = quikrCustomTrained(trainingmatrix,inputfasta,k,lambda)
+%xstar=quikrCustomTrained(traininmatrix,inputfasta,k,lambda) is the
+%implementation of qukir that lets you use a custom training matrix
+%"trainingmatrix" on the input data file "inputfasta" for the k-mer size
+%"k" (note this k-mer size must be such that the number of rows of
+%"trainingmatrix"=4^k), with the regularization value "lambda". The vector
+%of predicted concentrations "xstar" is returned on the same basis as
+%"trainingmatrix".
+if nargin~=4
+    error('There must be exactly 4 input arguments: the training matrix, the /path/to/input/fastafile, the k-mer size, and lambda');
+end
+
+[rws, clumns]=size(trainingmatrix); %get the size of the training matrix
+if rws~=4^k
+    error('Wrong k-mer size for input training matrix');
+end
+
+if (isunix && not(ismac))
+    [status, counts]=unix([sprintf('./count-linux -r %d -1 -u ',k) ' ' inputfasta]); %count the 6-mers in the fasta file, in the forward direction, return the counts without labels.
+     if status ~= 0
+        error('./count-linux failed: ensure count-linux is an executable. Try chmod a+rx count-linux. Be sure matlab/octave is in the same directory as count-linux');
+    end
+elseif ismac
+    [status, counts]=unix([sprintf('./count-osx -r %d -1 -u ',k) ' ' inputfasta]); %count the 6-mers in the fasta file, in the forward direction, return the counts without labels.
+    if status ~= 0
+        error('./count-osx failed: ensure count-linux is an executable. Try chmod a+rx count-osx. Be sure matlab/octave is in the same directory as count-osx');
+    end
+elseif ispc
+   error('Windows is not yet supported');
+end
+
+counts=textscan(counts,'%f'); %read them in as floats.
+counts=counts{:};
+counts=counts/sum(counts); %normalize the counts into a probability vector
+yaux=[0;lambda*counts]; %form the sample vector
+
+
+Aaux=[ones(1,clumns);lambda*trainingmatrix]; %form the k-mer sensing matrix
+warning off
+xstar=lsqnonneg(Aaux,yaux); %perform the non-negative lease squares
+warning on
+xstar=xstar/sum(xstar); %return the results as a probability vector 
\ No newline at end of file
-- 
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