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# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
# Biozentrum - University of Basel
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Unit tests for alignment fiddling.
"""
import unittest
from promod3 import modelling
from ost import seq, io
class ModellingTests(unittest.TestCase):
def testDeleteGapCols(self):
aln = io.LoadAlignment('data/double_gap_aln.fasta')
s0_orig = aln.GetSequence(0)
s1_orig = aln.GetSequence(1)
# recreate aln with added offsets and attach some random structure to
# both sequences
s0 = seq.CreateSequence(s0_orig.GetName(), str(s0_orig))
s1 = seq.CreateSequence(s1_orig.GetName(), str(s1_orig))
s0.SetOffset(1)
s1.SetOffset(2)
random_structure = io.LoadPDB('data/1CRN.pdb')
s0.AttachView(random_structure.CreateFullView())
s1.AttachView(random_structure.CreateFullView())
pimped_aln = seq.CreateAlignment()
pimped_aln.AddSequence(s0)
pimped_aln.AddSequence(s1)
processed_aln = modelling.DeleteGapCols(pimped_aln)
processed_s0 = processed_aln.GetSequence(0)
processed_s1 = processed_aln.GetSequence(1)
# the following things should be equal between sx and processed_sx:
# - name
# - offset
# - view attached
self.assertEqual(s0.GetName(), processed_s0.GetName())
self.assertEqual(s1.GetName(), processed_s1.GetName())
self.assertEqual(s0.GetOffset(), processed_s0.GetOffset())
self.assertEqual(s1.GetOffset(), processed_s1.GetOffset())
self.assertTrue(processed_s0.HasAttachedView())
self.assertTrue(processed_s1.HasAttachedView())
# the actual sequences changed and are checked with the expected outcome
self.assertEqual(str(processed_s0), 'ABCDEFG-H--I')
self.assertEqual(str(processed_s1), 'ABCDEFGHIJKL')
def testPullTerminalDeletions(self):
aln = io.LoadAlignment('data/terminal_deletion_aln.fasta')
# min_terminal_anchor_sizes which are <= 0 are disallowed
self.assertRaises(RuntimeError, modelling.PullTerminalDeletions, aln, -10)
self.assertRaises(RuntimeError, modelling.PullTerminalDeletions, aln, 0)
# check expected results for different min_terminal_anchor_sizes
# nothing should happen for anchor size 1
processed_aln = modelling.PullTerminalDeletions(aln, 1)
self.assertEqual(str(aln.GetSequence(0)), str(processed_aln.GetSequence(0)))
self.assertEqual(str(aln.GetSequence(1)), str(processed_aln.GetSequence(1)))
processed_aln = modelling.PullTerminalDeletions(aln, 2)
exp_s0 = 'GSHMG----DLK--------------YSLERLREILERLEENPSEKQIVEAIRAIVENNAQIVE--AAIE-NNAQIVENNRAIIEALEAIGVDQKILEEMKKQLKDLKRSLERG'
exp_s1 = '-----DAQDKLKYLVKQLERALRELKKSLDELERSLEELEKNPSEDALVENNRLNVENNKIIVEVLRIILE-------------------------------------------'
self.assertEqual(str(processed_aln.GetSequence(0)), exp_s0)
self.assertEqual(str(processed_aln.GetSequence(1)), exp_s1)
processed_aln = modelling.PullTerminalDeletions(aln, 3)
exp_s0 = 'GSHMG----DLK--------------YSLERLREILERLEENPSEKQIVEAIRAIVENNAQIVE--AAIE-NNAQIVENNRAIIEALEAIGVDQKILEEMKKQLKDLKRSLERG'
exp_s1 = '-----DAQDKLKYLVKQLERALRELKKSLDELERSLEELEKNPSEDALVENNRLNVENNKIIVEVLRIILE-------------------------------------------'
self.assertEqual(str(processed_aln.GetSequence(0)), exp_s0)
self.assertEqual(str(processed_aln.GetSequence(1)), exp_s1)
processed_aln = modelling.PullTerminalDeletions(aln, 4)
exp_s0 = 'GSHMG------------------DLKYSLERLREILERLEENPSEKQIVEAIRAIVENNAQIVE--AAIE-NNAQIVENNRAIIEALEAIGVDQKILEEMKKQLKDLKRSLERG'
exp_s1 = '-----DAQDKLKYLVKQLERALRELKKSLDELERSLEELEKNPSEDALVENNRLNVENNKIIVEVLRIILE-------------------------------------------'
self.assertEqual(str(processed_aln.GetSequence(0)), exp_s0)
self.assertEqual(str(processed_aln.GetSequence(1)), exp_s1)
processed_aln = modelling.PullTerminalDeletions(aln, 5)
exp_s0 = 'GSHMG------------------DLKYSLERLREILERLEENPSEKQIVEAIRAIVENNAQIVEAAIE---NNAQIVENNRAIIEALEAIGVDQKILEEMKKQLKDLKRSLERG'
exp_s1 = '-----DAQDKLKYLVKQLERALRELKKSLDELERSLEELEKNPSEDALVENNRLNVENNKIIVEVLRIILE-------------------------------------------'
self.assertEqual(str(processed_aln.GetSequence(0)), exp_s0)
self.assertEqual(str(processed_aln.GetSequence(1)), exp_s1)
# also check, whether sequence name, offsets and attached views are preserved
random_structure = io.LoadPDB('data/1CRN.pdb')
s0 = seq.CreateSequence(aln.GetSequence(0).GetName(), str(aln.GetSequence(0)))
s1 = seq.CreateSequence(aln.GetSequence(1).GetName(), str(aln.GetSequence(1)))
s0.AttachView(random_structure.CreateFullView())
s1.AttachView(random_structure.CreateFullView())
pimped_aln = seq.CreateAlignment()
pimped_aln.AddSequence(s0)
pimped_aln.AddSequence(s1)
processed_aln = modelling.PullTerminalDeletions(pimped_aln, 5)
processed_s0 = processed_aln.GetSequence(0)
processed_s1 = processed_aln.GetSequence(1)
# the following things should be equal between sx and processed_sx:
# - name
# - offset
# - view attached
self.assertEqual(s0.GetName(), processed_s0.GetName())
self.assertEqual(s1.GetName(), processed_s1.GetName())
self.assertEqual(s0.GetOffset(), processed_s0.GetOffset())
self.assertEqual(s1.GetOffset(), processed_s1.GetOffset())
self.assertTrue(processed_s0.HasAttachedView())
self.assertTrue(processed_s1.HasAttachedView())
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
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