quikr now works! the numbers are almost identical to matlab (is 6th digit precision an issue?). use a vflip and don't transpose and it works

2 files changed, 2 insertions, 2 deletions

diff --git a/quikr.py b/quikr.py
index 72a32f1..92c204b 100755
--- a/quikr.py
+++ b/quikr.py
@@ -84,9 +84,10 @@ def quikr(input_fasta_location, trained_matrix_location, kmer, default_lambda):
 
   #form the k-mer sensing matrix
   trained_matrix = trained_matrix * default_lambda;
-  trained_matrix = np.transpose(trained_matrix);
+  trained_matrix = np.flipud(trained_matrix);
   trained_matrix = np.vstack((np.ones(trained_matrix.shape[1]), trained_matrix))
 
+
   xstar, rnorm = scipy.optimize.nnls(trained_matrix, counts) 
 
   xstar = xstar / xstar.sum(0) 
diff --git a/quikr_train.py b/quikr_train.py
index b949589..6415f67 100755
--- a/quikr_train.py
+++ b/quikr_train.py
@@ -27,7 +27,6 @@ def main():
 
   # call the quikr train function, save the output with np.save
   matrix = quikr_train(args.input, args.kmer)
-  matrix = np.rot90(matrix)
 
   np.save(args.output, matrix)
   np.savetxt("python.csv", matrix, delimiter=",")