From 94d04a1e503121a98b403f882c18a4f0799267d7 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 29 Jan 2014 11:53:30 -0500
Subject: add filtering based on consecutive mer lengths

---
 src/max_consecutive_bindings.py | 54 -----------------------------------------
 1 file changed, 54 deletions(-)
 delete mode 100644 src/max_consecutive_bindings.py

(limited to 'src/max_consecutive_bindings.py')

diff --git a/src/max_consecutive_bindings.py b/src/max_consecutive_bindings.py
deleted file mode 100644
index a2e6c8d..0000000
--- a/src/max_consecutive_bindings.py
+++ /dev/null
@@ -1,54 +0,0 @@
-import sys
-
-binding = { 'A': 'T', 'T': 'A',	'C': 'G', 'G': 'C',	'_': False }
-
-
-def max_consecutive_bindings(mer1, mer2):
-	if len(mer2) > len(mer1):
-		mer1, mer2 = mer2, mer1
-	
-	# reverse mer2,
-	mer2 = mer2[::-1]
-	mer1 = mer1.ljust(len(mer1) + len(mer1), "_")
-
-	max_bind = 0;
-	for offset in range(len(mer2)):
-		consecutive = 0
-		for x in range(len(mer2)):
-			if binding[mer1[offset+x]] == mer2[x]:
-					consecutive = consecutive + 1
-			else:
-				consecutive = 0
-
-			max_bind = max(consecutive,max_bind)
-
-	return max_bind
-
-def test():
-	# mer 1  				 mer 2					# correct ans
-	arr = [
-	("ATATAT",			 "TATATA", 					5),
-	("ACAGGGAT",		 "ATATATAT", 				2),
-	("CATATATAT", 	 "ATATATATATAT",	  8),
-	("ATATATATATAT", "ATATATATAT", 		 10),
-	("ATATAT",			 "TATAT",					  5),
-	("AACGATACCATG", "GGATCATACGTA", 		3),
-	("CGT",          "ACG",			 				3),
-	("ACG",          "CGT",			 				3),
-	("CACC", 				 "GGTGT", 					4),
-	("GGTGT", 			 "CACC", 					4),
-	]
-	
-	print 'pass\tmer1\tmer2\tres\tcorr'
-	for mer_combination in arr:
-		response = []
-		ans = max_consecutive_bindings(mer_combination[0], mer_combination[1])
-	
-		response.append(str(ans == mer_combination[2]))
-		response.append(mer_combination[0])
-		response.append(mer_combination[1])
-		response.append(str(ans))
-		response.append(str(mer_combination[2]))
-	
-		print '\t'.join(response)
-	
-- 
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