Author: bugman
Date: Thu Jan 22 17:21:34 2015
New Revision: 27276
URL: http://svn.gna.org/viewcvs/relax?rev=27276&view=rev
Log:
Added the end gap penalty arguments to
lib.sequence_alignment.align_protein.align_pairwise().
Modified:
trunk/lib/sequence_alignment/align_protein.py
Modified: trunk/lib/sequence_alignment/align_protein.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/align_protein.py?rev=27276&r1=27275&r2=27276&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/align_protein.py (original)
+++ trunk/lib/sequence_alignment/align_protein.py Thu Jan 22 17:21:34 2015
@@ -32,23 +32,27 @@
from lib.sequence_alignment.substitution_matrices import BLOSUM62, BLOSUM62_SEQ
-def align_pairwise(sequence1, sequence2, algorithm='NW70', matrix='BLOSUM62',
gap_open_penalty=1.0, gap_extend_penalty=1.0):
+def align_pairwise(sequence1, sequence2, algorithm='NW70', matrix='BLOSUM62',
gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0):
"""Align two protein sequences.
- @param sequence1: The first protein sequence as one letter
codes.
- @type sequence1: str
- @param sequence2: The second protein sequence as one letter
codes.
- @type sequence2: str
- @keyword algorithm: The alignment algorithm to use.
- @type algorithm: str
- @keyword matrix: The substitution matrix to use.
- @type matrix: 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 protein sequence as one
letter codes.
+ @type sequence1: str
+ @param sequence2: The second protein sequence as one
letter codes.
+ @type sequence2: str
+ @keyword algorithm: The alignment algorithm to use.
+ @type algorithm: str
+ @keyword matrix: The substitution matrix to use.
+ @type matrix: 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
"""
# Checks.
@@ -78,7 +82,7 @@
# The alignment.
if algorithm == 'NW70':
- align1, align2, gaps = needleman_wunsch_align(sequence1, sequence2,
sub_matrix=sub_matrix, sub_seq=sub_seq, gap_open_penalty=gap_open_penalty,
gap_extend_penalty=gap_extend_penalty)
+ align1, align2, gaps = needleman_wunsch_align(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)
# Final printout.
sys.stdout.write("\n%-30s %s\n" % ("Aligned sequence 1:", align1))
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