From d3a935d76bc5ee6c211184c50790e6576654ca67 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 6 Mar 2014 20:37:04 -0500 Subject: UNVERIFIED but progress on converting quikr.m to dna-utils --- src/matlab/quikrCustomTrained.m | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src/matlab/quikrCustomTrained.m') diff --git a/src/matlab/quikrCustomTrained.m b/src/matlab/quikrCustomTrained.m index 9331e06..9a45256 100644 --- a/src/matlab/quikrCustomTrained.m +++ b/src/matlab/quikrCustomTrained.m @@ -15,9 +15,9 @@ if rows~=4^k error('Wrong k-mer size for input training matrix'); end -[status, counts]=unix([sprintf('count-kmers -r %d -1 -u ', k) ' ' inputfasta]); %count the k-mers in the fasta file, in the forward direction, return the counts without labels. +[status, counts]=unix([sprintf('kmer_total_count -k %d', k) ' -i ' inputfasta]); %count the k-mers in the fasta file, in the forward direction, return the counts without labels. if status ~= 0 - error('count-kmers failed: ensure count-kmers is in your path.'); + error('kmer_total_count failed: ensure kmer_total_count is in your path.'); end counts=textscan(counts,'%f'); %read them in as floats. -- cgit v1.2.3