Update multifasta_to_otu.py for new quikr function

  * Removed an old comment from the quikr function
  * Load the trained matrix from multifasta main.
  * This will reduce load times as we only need
    to call it once

2 files changed, 3 insertions, 4 deletions

diff --git a/multifasta_to_otu.py b/multifasta_to_otu.py
index 4a46be6..3e14fcf 100755
--- a/multifasta_to_otu.py
+++ b/multifasta_to_otu.py
@@ -12,7 +12,6 @@ import platform
 # our defaults
 kmer = 6
 lamb = 10000
-trained_matrix = ""
 output_directory = ""
 input_directory = ""
 
@@ -65,6 +64,9 @@ def main():
   if args.kmer is not None:
     kmer = args.kmer
 
+  # Load trained matrix
+  trained_matrix = np.load(args.trained_matrix);
+
   fasta_list = os.listdir(args.input_directory)
 
   pool = Pool(processes=jobs)
diff --git a/quikr.py b/quikr.py
index 065590d..a6b8bd0 100755
--- a/quikr.py
+++ b/quikr.py
@@ -85,9 +85,6 @@ def quikr(input_fasta_location, trained_matrix, kmer, default_lambda):
   counts = default_lambda * counts
   counts = np.concatenate([np.zeros(1), counts])
 
-  # load our trained matrix
-
-
   #form the k-mer sensing matrix
   trained_matrix = trained_matrix * default_lambda;
   trained_matrix = np.flipud(trained_matrix);