diff options
| -rwxr-xr-x | quikr.py | 10 |
1 files changed, 8 insertions, 2 deletions
@@ -47,7 +47,13 @@ def main(): np.savetxt(args.output, xstar, delimiter=",", fmt="%f") return 0 -def quikr(input_fasta_location, trained_matrix_location, kmer, default_lambda): +def quikr_load_trained_matrix_from_file(input_fasta_location, trained_matrix_location, kmer, default_lambda): + + trained_matrix = np.load(trained_matrix_location) + xstar = quikr(input_fasta_location, trained_matrix, kmer, default_lambda) + return xstar + +def quikr(input_fasta_location, trained_matrix, kmer, default_lambda): """ input_fasta is the input fasta file to find the estimated frequencies of trained_matrix is the trained matrix we are using to estimate the species @@ -80,7 +86,7 @@ def quikr(input_fasta_location, trained_matrix_location, kmer, default_lambda): counts = np.concatenate([np.zeros(1), counts]) # load our trained matrix - trained_matrix = np.load(trained_matrix_location) + #form the k-mer sensing matrix trained_matrix = trained_matrix * default_lambda; |