Author: bugman
Date: Fri Jan 30 11:33:40 2015
New Revision: 27383
URL: http://svn.gna.org/viewcvs/relax?rev=27383&view=rev
Log:
Created the Test_seq_align.test_alignment_addition unit test.
This is in the _data_store.test_seq_align unit test module. This tests the
setup of the sequence
alignment object via the data_store.seq_align.Sequence_alignment.add() method.
Added:
trunk/test_suite/unit_tests/_data_store/test_seq_align.py
Modified:
trunk/test_suite/unit_tests/_data_store/__init__.py
Modified: trunk/test_suite/unit_tests/_data_store/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_data_store/__init__.py?rev=27383&r1=27382&r2=27383&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_data_store/__init__.py (original)
+++ trunk/test_suite/unit_tests/_data_store/__init__.py Fri Jan 30 11:33:40
2015
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007 Edward d'Auvergne
#
+# Copyright (C) 2007-2015 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -19,6 +19,9 @@
#
#
###############################################################################
-__all__ = ['test___init__',
- 'test_diff_tensor',
- 'test_mol_res_spin']
+__all__ = [
+ 'test___init__',
+ 'test_diff_tensor',
+ 'test_mol_res_spin',
+ 'test_seq_align'
+]
Added: trunk/test_suite/unit_tests/_data_store/test_seq_align.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_data_store/test_seq_align.py?rev=27383&view=auto
==============================================================================
--- trunk/test_suite/unit_tests/_data_store/test_seq_align.py (added)
+++ trunk/test_suite/unit_tests/_data_store/test_seq_align.py Fri Jan 30
11:33:40 2015
@@ -0,0 +1,122 @@
+###############################################################################
+#
#
+# Copyright (C) 2015 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Python module imports.
+from unittest import TestCase
+
+# relax module imports.
+from data_store.seq_align import Sequence_alignments
+
+
+class Test_seq_align(TestCase):
+ """Unit tests for the data.seq_align relax module."""
+
+
+ def setUp(self):
+ """Set 'self.seq_align' to an empty instance of the
Sequence_alignments class."""
+
+ self.seq_align = Sequence_alignments()
+
+
+ def test_alignment_addition(self):
+ """Test the creation of a new sequence alignment object."""
+
+ # The data.
+ object_ids = ['frame_order', 'ensemble', 'ensemble', 'ensemble',
'ensemble', 'ensemble', 'ensemble', 'ensemble']
+ models = [None, 1, 1, 1, 1, 1, 1, 1]
+ molecules = [
+ 'N-dom',
+ 'ensemble 4M A',
+ 'ensemble 4M B',
+ 'ensemble 4M C',
+ 'ensemble 4M D',
+ 'CaM-IQ A',
+ 'CaM-IQ B',
+ 'CaM-IQ C'
+ ]
+ sequences = [
+
'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK*****',
+
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
+
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
+
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
+
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
+ '
QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
+ '
LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
+ '
LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
+
+ 'TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG',
+
'ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKM',
+
'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR'
+ ]
+ strings = [
+
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK------------------------------------------------------------------------*****----------------------------------------------------------------------------',
+
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----------------------------------------------------------------------------MKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
+
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
+
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
+
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
+
'--QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----MKSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
+
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----MKDEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
+
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK-------EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
+ ]
+ gaps = []
+ for i in range(len(strings)):
+ gaps.append([])
+ for j in range(len(strings[0])):
+ if strings[i][j] == '-':
+ gaps[i].append(1)
+ else:
+ gaps[i].append(0)
+ msa_algorithm = 'Central Star'
+ pairwise_algorithm = 'NW70'
+ matrix = 'BLOSUM62'
+ gap_open_penalty = 10.0
+ gap_extend_penalty = 1.0
+ end_gap_open_penalty = 0.0
+ end_gap_extend_penalty = 0.0
+
+ # Add the alignment.
+ self.seq_align.add(object_ids=object_ids, models=models,
molecules=molecules, sequences=sequences, strings=strings, gaps=gaps,
msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm,
matrix=matrix, 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 expected IDs.
+ ids = []
+ for i in range(len(object_ids)):
+ ids.append("Object '%s'" % object_ids[i])
+ if models[i] != None:
+ ids[-1] += "; Model %i" % models[i]
+ ids[-1] += "; Molecule '%s'" % molecules[i]
+
+ # Check the data.
+ for i in range(8):
+ print("Checking \"%s\"" % ids[i])
+ self.assertEqual(self.seq_align[0].ids[i], ids[i])
+ self.assertEqual(self.seq_align[0].object_ids[i], object_ids[i])
+ self.assertEqual(self.seq_align[0].models[i], models[i])
+ self.assertEqual(self.seq_align[0].molecules[i], molecules[i])
+ self.assertEqual(self.seq_align[0].sequences[i], sequences[i])
+ self.assertEqual(self.seq_align[0].strings[i], strings[i])
+ self.assertEqual(self.seq_align[0].gaps[i], gaps[i])
+ self.assertEqual(self.seq_align[0].msa_algorithm, msa_algorithm)
+ self.assertEqual(self.seq_align[0].pairwise_algorithm,
pairwise_algorithm)
+ self.assertEqual(self.seq_align[0].matrix, matrix)
+ self.assertEqual(self.seq_align[0].gap_open_penalty,
gap_open_penalty)
+ self.assertEqual(self.seq_align[0].gap_extend_penalty,
gap_extend_penalty)
+ self.assertEqual(self.seq_align[0].end_gap_open_penalty,
end_gap_open_penalty)
+ self.assertEqual(self.seq_align[0].end_gap_extend_penalty,
end_gap_extend_penalty)
r27383 - in /trunk/test_suite/unit_tests/_data_store: __init__.py test_seq_align.py