do the matrix rotations and manipulations in quikr_train instead of quikr

2 files changed, 4 insertions, 3 deletions

diff --git a/quikr.py b/quikr.py
index b40f1f6..a2b4fcf 100755
--- a/quikr.py
+++ b/quikr.py
@@ -87,7 +87,6 @@ def quikr(input_fasta_location, trained_matrix, kmer, default_lambda):
 
   #form the k-mer sensing matrix
   trained_matrix = trained_matrix * default_lambda;
-  trained_matrix = np.flipud(trained_matrix);
   trained_matrix = np.vstack((np.ones(trained_matrix.shape[1]), trained_matrix))
 
 
diff --git a/quikr_train.py b/quikr_train.py
index ba139eb..b86afb9 100755
--- a/quikr_train.py
+++ b/quikr_train.py
@@ -55,11 +55,13 @@ def quikr_train(input_file_location, kmer):
     input_file = Popen(["./probabilities-by-read-osx", str(kmer), input_file_location, kmer_file_name]) 
 
   # load and  normalize the matrix by dividing each element by the sum of it's column.
+  # also do some fancy rotations so that it works properly with quikr
   matrix  = np.loadtxt(input_file.stdout)
   
   matrix = np.rot90(matrix)
-  normalized = matrix / matrix.sum(0)
-  return normalized
+  matrix = matrix / matrix.sum(0)
+  matrix = np.flipud(matrix);
+  return matrix
   
 if __name__ == "__main__":
     sys.exit(main())