Author: bugman
Date: Thu Jan 29 13:23:58 2015
New Revision: 27345
URL: http://svn.gna.org/viewcvs/relax?rev=27345&view=rev
Log:
Simplified the Test_coordinates.test_common_residues unit test by removing many
residues.
This is from the _lib._structure._internal.test_coordinates unit test module.
Modified:
trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
Modified:
trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py?rev=27345&r1=27344&r2=27345&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
(original)
+++ trunk/test_suite/unit_tests/_lib/_structure/_internal/test_coordinates.py
Thu Jan 29 13:23:58 2015
@@ -36,30 +36,39 @@
# The gap matrices.
gap_matrices = [
array([
- [1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1],
- [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0]
+ [1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
], int16),
array([
- [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1],
- [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+ [1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1],
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0]
], int16)
]
- seq1 = 'TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG**'
- seq2 =
'ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKM**'
- seq3 =
'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR**'
+ seq1 = 'TEEQVDADGGT'
+ seq2 = 'ADQLTEEQVDADGNGTIDFPEFLTMMARKM'
+ seq3 = 'LTEEQMINEVDAGNGTIDFPEFLTMMAR'
# Determine the common residues.
- skip = coordinates.common_residues(gap_matrices=gap_matrices,
one_letter_codes=[seq1, seq2, seq3])
+ skip, gapped_strings =
coordinates.common_residues(gap_matrices=gap_matrices, one_letter_codes=[seq1,
seq2, seq3], seq=True)
# The expected skipping matrices.
N = len(seq1)
skip_real = [
- [0]*N,
+ [0]*4 + [1]*4 + [0]*(N-8),
[1]*4 + [0]*N + [1]*(len(seq2)-N-4),
[1] + [0]*N + [1]*(len(seq3)-N-1)
]
+
+ # The expected gapped strings.
+ gapped_seq1 = '----TEEQ----VDA-G-GT----------------'
+ gapped_seq2 = '----TEEQ----VDA-G-GT----------------'
+ gapped_seq3 = '----TEEQMINEVDA-G-GT----------------'
+ gapped_real = [gapped_seq1, gapped_seq2, gapped_seq3]
# Checks.
for i in range(3):
print("Sequence %i" % (i+1))
self.assertEqual(len(skip_real[i]), len(skip[i]))
+ for j in range(len(skip_real[i])):
+ self.assertEqual(skip_real[i][j], skip[i][j])
+ #self.assertEqual(gapped_real[i], gapped_strings[i])
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