Author: bugman
Date: Thu Jan 29 15:53:41 2015
New Revision: 27358
URL: http://svn.gna.org/viewcvs/relax?rev=27358&view=rev
Log:
Fixes for the unit tests of the _lib._sequence_alignment.test_needleman_wunsch
module.
The lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function
now returns the
alignment score.
Modified:
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py
Modified:
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py?rev=27358&r1=27357&r2=27358&view=diff
==============================================================================
---
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py
(original)
+++
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py
Thu Jan 29 15:53:41 2015
@@ -41,8 +41,9 @@
print(seq2)
# Perform the alignment.
- align1, align2, gaps = needleman_wunsch_align(seq1, seq2,
sub_matrix=SIMILARITY_DNA, sub_seq=SIMILARITY_DNA_SEQ, gap_open_penalty=1,
gap_extend_penalty=1)
+ score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2,
sub_matrix=SIMILARITY_DNA, sub_seq=SIMILARITY_DNA_SEQ, gap_open_penalty=1,
gap_extend_penalty=1)
print("\nOut:")
+ print(score)
print(align1)
print(align2)
print(gaps)
@@ -81,8 +82,9 @@
print(seq2)
# Perform the alignment.
- align1, align2, gaps = needleman_wunsch_align(seq1, seq2,
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5,
gap_extend_penalty=1)
+ score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2,
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5,
gap_extend_penalty=1)
print("\nOut:")
+ print(score)
print(align1)
print(align2)
print(gaps)
@@ -121,8 +123,9 @@
print(seq2)
# Perform the alignment.
- align1, align2, gaps = needleman_wunsch_align(seq1, seq2,
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5,
gap_extend_penalty=1)
+ score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2,
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5,
gap_extend_penalty=1)
print("\nOut:")
+ print(score)
print(align1)
print(align2)
print(gaps)
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