Author: bugman
Date: Thu Jan 29 15:36:05 2015
New Revision: 27353
URL: http://svn.gna.org/viewcvs/relax?rev=27353&view=rev
Log:
The Needleman-Wunsch sequence alignment algorithm now calculates and returns an
alignment score.
This is in the lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align()
function. The score
is calculated as the sum of the Needleman-Wunsch matrix elements along the
traceback path.
Modified:
trunk/lib/sequence_alignment/needleman_wunsch.py
Modified: trunk/lib/sequence_alignment/needleman_wunsch.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/needleman_wunsch.py?rev=27353&r1=27352&r2=27353&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/needleman_wunsch.py (original)
+++ trunk/lib/sequence_alignment/needleman_wunsch.py Thu Jan 29 15:36:05 2015
@@ -63,8 +63,8 @@
@type end_gap_open_penalty: float
@keyword end_gap_extend_penalty: The optional penalty for extending a
gap at the end of a sequence.
@type end_gap_extend_penalty: float
- @return: The two alignment strings and the gap
matrix.
- @rtype: str, str, numpy rank-2 int array
+ @return: The alignment score, two alignment
strings and the gap matrix.
+ @rtype: float, str, str, numpy rank-2 int array
"""
# The sequence lengths.
@@ -83,6 +83,7 @@
matrix, traceback_matrix = needleman_wunsch_matrix(sequence1, sequence2,
sub_matrix=sub_matrix, sub_seq=sub_seq, gap_open_penalty=gap_open_penalty,
gap_extend_penalty=gap_extend_penalty,
end_gap_open_penalty=end_gap_open_penalty,
end_gap_extend_penalty=end_gap_extend_penalty)
# Generate the alignment.
+ score = 0.0
i = M - 1
j = N - 1
alignment1 = ""
@@ -115,6 +116,9 @@
if i < 0 and j < 0:
break
+ # Update the total score.
+ score += matrix[i, j]
+
# Reverse the alignments.
align1 = alignment1[::-1]
align2 = alignment2[::-1]
@@ -128,7 +132,7 @@
gaps[1, l] = 1
# Return the alignments and gap matrix.
- return align1, align2, gaps
+ return score, align1, align2, gaps
def needleman_wunsch_matrix(sequence1, sequence2, sub_matrix=None,
sub_seq=None, gap_open_penalty=SCORE_GAP_PENALTY, gap_extend_penalty=1.0,
end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0, epsilon=1e-7):
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