From 7ae39dc8d0cb12a2db7477fb91782f29c273d151 Mon Sep 17 00:00:00 2001 From: Calvin Date: Fri, 15 Mar 2013 16:43:04 -0400 Subject: eliminated the need for Nmers.txt:-) --- src/python/quikr.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/quikr.py b/src/python/quikr.py index 182fd74..225ea9b 100755 --- a/src/python/quikr.py +++ b/src/python/quikr.py @@ -62,7 +62,7 @@ def train_matrix(input_file_location, kmer): print "could not find kmer file" exit() - input_file = Popen(["probabilities-by-read", str(kmer), input_file_location, kmer_file_name] , stdout=PIPE) + input_file = Popen(["bash", "-c", "probabilities-by-read " + str(kmer) + " " + input_file_location + " <(generate_kmers 6)"], stdout=PIPE) # 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 -- cgit v1.2.3