Author: bugman
Date: Thu Jan 22 17:20:07 2015
New Revision: 27275
URL: http://svn.gna.org/viewcvs/relax?rev=27275&view=rev
Log:
The needleman_wunsch_align() function now accepts the end gap penalty arguments.
These are passed onto the needleman_wunsch_matrix() function.
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=27275&r1=27274&r2=27275&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/needleman_wunsch.py (original)
+++ trunk/lib/sequence_alignment/needleman_wunsch.py Thu Jan 22 17:20:07 2015
@@ -41,26 +41,30 @@
TRACEBACK_LEFT = 2
-def needleman_wunsch_align(sequence1, sequence2, sub_matrix=None,
sub_seq=None, gap_open_penalty=SCORE_GAP_PENALTY, gap_extend_penalty=1.0):
+def needleman_wunsch_align(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):
"""Align two sequences using the Needleman-Wunsch algorithm using the
EMBOSS logic for extensions.
This is implemented as described in the U{Wikipedia article on the
Needleman-Wunsch algorithm
<https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm>}. The
algorithm has been modified to match that of
U{EMBOSS<http://emboss.sourceforge.net/>} to allow for gap opening and
extension penalties, as well as end penalties.
- @param sequence1: The first sequence.
- @type sequence1: str
- @param sequence2: The second sequence.
- @type sequence2: str
- @keyword sub_matrix: The substitution matrix to use to
determine the penalties.
- @type sub_matrix: numpy rank-2 int array
- @keyword sub_seq: The one letter code sequence corresponding
to the substitution matrix indices.
- @type sub_seq: str
- @keyword gap_open_penalty: The penalty for introducing gaps, as a
positive number.
- @type gap_open_penalty: float
- @keyword gap_extend_penalty: The penalty for extending a gap, as a
positive number.
- @type gap_extend_penalty: float
- @return: The two alignment strings and the gap
matrix.
- @rtype: str, str, numpy rank-2 int array
+ @param sequence1: The first sequence.
+ @type sequence1: str
+ @param sequence2: The second sequence.
+ @type sequence2: str
+ @keyword sub_matrix: The substitution matrix to use to
determine the penalties.
+ @type sub_matrix: numpy rank-2 int array
+ @keyword sub_seq: The one letter code sequence
corresponding to the substitution matrix indices.
+ @type sub_seq: str
+ @keyword gap_open_penalty: The penalty for introducing gaps, as a
positive number.
+ @type gap_open_penalty: float
+ @keyword gap_extend_penalty: The penalty for extending a gap, as a
positive number.
+ @type gap_extend_penalty: float
+ @keyword end_gap_open_penalty: The optional penalty for opening a gap
at the end of a sequence.
+ @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
"""
# The sequence lengths.
@@ -76,7 +80,7 @@
raise RelaxError("The residue '%s' from the second sequence cannot
be found in the substitution matrix residues '%s'." % (sequence2[j], sub_seq))
# Calculate the scoring and traceback matrices.
- 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)
+ 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.
i = M - 1
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