From c46ba680ed29676e7d61a836585f3225b5916276 Mon Sep 17 00:00:00 2001
From: mutantturkey <mutantturke@gmail.com>
Date: Tue, 19 Feb 2013 08:42:58 -0500
Subject: added argument to accept output (solution vector) into a csv

---
 quikr.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/quikr.py b/quikr.py
index 25eb75b..4595b48 100755
--- a/quikr.py
+++ b/quikr.py
@@ -18,6 +18,7 @@ def main():
     matrix.")
 
     parser.add_argument("-f", "--fasta", help="path to a fasta file", required=True)
+    parser.add_argument("-o", "--output", help="the path to write your probability vector (csv output)", required=True)
     parser.add_argument("-t", "--trained-matrix", help="path to a custom trained matrix")
     parser.add_argument("-l", "--lamb", type=int, help="the default lambda value is 10,000")
     parser.add_argument("-k", "--kmer", type=int, 
@@ -52,7 +53,7 @@ def main():
         input_lambda = 10000
         kmer = 6
     xstar = quikr(args.fasta, trained_matrix_location, kmer, input_lambda)
-    np.savetxt("python.csv", xstar, delimiter=",")
+    np.savetxt("args.output, xstar, delimiter=",")
     print xstar 
     return 0
 
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