Author: bugman
Date: Thu Jan 29 19:18:23 2015
New Revision: 27371
URL: http://svn.gna.org/viewcvs/relax?rev=27371&view=rev
Log:
Improvement for the lib.sequence_alignment.msa.central_star() function.
The strings and gap matrix returned by the function have been reordered to
match the input
sequences.
Modified:
trunk/lib/sequence_alignment/msa.py
Modified: trunk/lib/sequence_alignment/msa.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/msa.py?rev=27371&r1=27370&r2=27371&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/msa.py (original)
+++ trunk/lib/sequence_alignment/msa.py Thu Jan 29 19:18:23 2015
@@ -141,12 +141,19 @@
# Rebuild the alignment lists and create a gap matrix.
strings = []
M = len(Sc_prime)
- gaps = zeros((N, M), int16)
strings.append(Sc_prime)
for i in range(N-1):
strings.append(''.join(string_lists[i]))
for i in range(N):
strings[i] = strings[i].replace('X', '-')
+
+ # Restore the original sequence ordering.
+ string = strings.pop(0)
+ strings.insert(Sc_index, string)
+
+ # Create the gap matrix.
+ gaps = zeros((N, M), int16)
+ for i in range(N):
for j in range(M):
if strings[i][j] == '-':
gaps[i, j] = 1
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