r27264 - /trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py -- January 22, 2015 - 15:53

Author: bugman
Date: Thu Jan 22 15:53:43 2015
New Revision: 27264

URL: http://svn.gna.org/viewcvs/relax?rev=27264&view=rev
Log:
Updated the gap penalties in the Test_align_protein.test_align_pairwise unit 
test.

This is from the unit test module _lib._sequence_alignment.test_align_protein.


Modified:
    trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py

Modified: 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py?rev=27264&r1=27263&r2=27264&view=diff
==============================================================================
--- 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py  
(original)
+++ 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py  
Thu Jan 22 15:53:43 2015
@@ -38,13 +38,13 @@
             - 
'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla',
             - 
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'.
 
-        From online servers, the results should be::
-        
+        From online servers, the results with a gap open penalty of 5 and 
gap extend of 1 should be::
+
             https://www.ebi.ac.uk/Tools/psa/emboss_needle/
             EMBOSS_001           
IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKLA
-                                 :|||:|||:|||:|| | |   ||||||||||:|.. 
.|:|:||||||||:||:.|::|.:|:|.|| 
+                                 :|||:|||:|||:|| | |   ||||||||||:|.. 
.|:|:||||||||:||:.|::|.:|:|.||
             EMBOSS_001           
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-
-            
+
             http://web.expasy.org/cgi-bin/sim/sim.pl?prot
             UserSeq1             
IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKL
             UserSeq2             
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL
@@ -57,8 +57,8 @@
         print(seq1)
         print(seq2)
 
-        # Perform the alignment. 
-        align1, align2, gaps = align_pairwise(seq1, seq2, matrix='BLOSUM62', 
gap_penalty=10.0)
+        # Perform the alignment.
+        align1, align2, gaps = align_pairwise(seq1, seq2, matrix='BLOSUM62', 
gap_open_penalty=5.0, gap_extend_penalty=1.0)
         print(align1)
         print(align2)
         print(gaps)