have matlab use global executables

3 files changed, 12 insertions, 37 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

diff --git a/src/matlab/quikrCustomTrained.m b/src/matlab/quikrCustomTrained.m
index b58aa31..c7961c7 100644
--- a/src/matlab/quikrCustomTrained.m
+++ b/src/matlab/quikrCustomTrained.m
@@ -15,19 +15,9 @@ 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

+[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'); %read them in as floats.

 counts=counts{:};

@@ -39,4 +29,4 @@ 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
+xstar=xstar/sum(xstar); %return the results as a probability vector 

diff --git a/src/matlab/quikrTrain.m b/src/matlab/quikrTrain.m
index 7960cca..abdba95 100644
--- a/src/matlab/quikrTrain.m
+++ b/src/matlab/quikrTrain.m
@@ -21,13 +21,7 @@ outputfilename=fullfile(pathtofile, [filename sprintf('-sensingmatrixK%d.txt',k)
 

 kmerfilename=sprintf('%dmers.txt',k); %This contains the list of 6-mers to count. In future versions this will be computed locally instead of being read in.

 

-if (isunix && not(ismac)) %this is for the linux version

-    unix(['./probabilities-by-read-linux ' sprintf('%d',k) ' ' inputfasta ' ' kmerfilename ' > ' outputfilename]); %obtain the k-mer counts of the inputfasta read-by-read

-elseif ismac %mac version

-    unix(['./probabilities-by-read-osx ' sprintf('%d',k) ' ' inputfasta ' ' kmerfilename ' > ' outputfilename]); %obtain the k-mer counts of the inputfasta read-by-read

-elseif ispc %No PC version

-    error('Windows is not yet supported');

-end

+unix(['probabilities-by-read ' sprintf('%d',k) ' ' inputfasta ' ' kmerfilename ' > ' outputfilename]); %obtain the k-mer counts of the inputfasta read-by-read

 

 fid=fopen(outputfilename); %open the output file