diff options
| -rwxr-xr-x | quikr.py | 1 | ||||
| -rwxr-xr-x | quikr_train.py | 6 |
2 files changed, 4 insertions, 3 deletions
@@ -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()) |