multifasta_to_otu.py support for compression

2 files changed, 8 insertions, 2 deletions

diff --git a/multifasta_to_otu.py b/multifasta_to_otu.py
index 548633e..bcc8177 100755
--- a/multifasta_to_otu.py
+++ b/multifasta_to_otu.py
@@ -5,7 +5,9 @@ from Bio import SeqIO
 import multiprocessing
 from subprocess import *
 import os
+import gzip
 import quikr as q
+import quikr_util as qu
 import sys
 import numpy as np
 import argparse
@@ -70,7 +72,12 @@ def main():
     kmer = args.kmer
 
   # Load trained matrix
-  trained_matrix = np.load(args.trained_matrix)
+  if qu.isCompressed(args.trained_matrix):
+    trained_matrix_file = gzip.open(args.trained_matrix, "rb")
+  else:
+    trained_matrix_file = open(args.trained_matrix, "rb")
+  
+  trained_matrix = np.load(trained_matrix_file)
 
   # Return a list of the input directory
   fasta_list = os.listdir(args.input_directory)
diff --git a/quikr.py b/quikr.py
index 401b5ca..f83cdf2 100755
--- a/quikr.py
+++ b/quikr.py
@@ -52,7 +52,6 @@ def main():
 def quikr_load_trained_matrix_from_file(input_fasta_location, trained_matrix_location, kmer, default_lambda):
   
   if qu.isCompressed(trained_matrix_location):
-    print "compressed!"
     trained_matrix_file = gzip.open(trained_matrix_location, "rb")
   else:
     trained_matrix_file = open(trained_matrix_location, "rb")