have matlab use global executables

1 files changed, 7 insertions, 16 deletions

diff --git a/src/matlab/quikr.m b/src/matlab/quikr.m
index d24596e..f43ae8f 100644
--- a/src/matlab/quikr.m
+++ b/src/matlab/quikr.m
@@ -12,21 +12,12 @@ function xstar = quikr(inputfasta)
 %orientation, so as a preprocessing step, make sure everything is in the

 %forward (+) orientation.

 if nargin>1

-    error('too many input arguments');

-end

-if (isunix && not(ismac))   %If linux, use ./count-linux

-    [status, counts]=unix(['./count-linux -r 6 -1 -u ' 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 %If mac, then use ./count-osx

-    [status, counts]=unix(['./count-osx -r 6 -1 -u ' 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    

+  error('too many input arguments');

+

+[status, counts]=unix(['count-kmers -r 6 -1 -u ' inputfasta]); %count the 6-mers in the fasta file, in the forward direction, return the counts without labels

+if status ~= 0

+  error('count-kmers failed: ensure count-kmers is in your path.');

+

 counts=textscan(counts,'%f'); %convert into floats

 counts=counts{:}; %make into a vector

 counts=counts/sum(counts); %form a probability vector from the counts

@@ -49,4 +40,4 @@ end %Matlab automatically reads it in correctly, just need to rename it
 warning off

 xstar=lsqnonneg(Aaux,yaux); %perform the nonnegative least squares

 warning on

-xstar=xstar/sum(xstar); %transform the output into a probability vector. Note this vector is on the same basis as Aaux, so the entries correspond to sequences in trainset7_112011.fa
\ No newline at end of file
+xstar=xstar/sum(xstar); %transform the output into a probability vector. Note this vector is on the same basis as Aaux, so the entries correspond to sequences in trainset7_112011.fa