From 8ff88529a71144e15b701b75ed6b24d31b5995a0 Mon Sep 17 00:00:00 2001
From: farahzk <fzkhan2@illinios.edu>
Date: Wed, 5 Mar 2014 02:29:16 -0600
Subject: [PATCH] Create NeedlemanWunsch.py

This version takes two input files along with a similarity score matrix and gap penalty through terminal/command line
---
 NeedlemanWunsch.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 NeedlemanWunsch.py

diff --git a/NeedlemanWunsch.py b/NeedlemanWunsch.py
new file mode 100644
index 0000000..b0fa863
--- /dev/null
+++ b/NeedlemanWunsch.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+
+import sys, string
+import alignment #import the file with the functions
+
+# Command-line arguments for 3 files and one integer.
+f1 = open(sys.argv[1], 'r') #first fasta/txt file
+f1.readline()
+seq1 = ''
+for line in f1:
+    seq1 += string.strip(line)
+
+f2 = open(sys.argv[2], 'r') #second fasta/txt file
+seq2 = ''
+f2.readline()
+for line in f2:
+    seq2 += string.strip(line)
+
+alignment.needleWunsch(seq1, seq2, sys.argv[3], int(sys.argv[4]))
+# sys.argv[3]=substitution matrix file
+# sys.argv[4]=gap_penalty.