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import sys
import unittest
from ost import *
from ost import settings
from ost import seq
from ost.bindings.clustalw import *
from ost.seq.alg import renumber
try:
clustalw_path=settings.Locate(('clustalw', 'clustalw2'))
except(settings.FileNotFound):
clustalw_path=None
class TestRenumber(unittest.TestCase):
def setUp(self):
self.target_seq = io.LoadSequence("testfiles/peptide.fasta")
self.peptide_original = io.LoadEntity("testfiles/peptide_original.pdb")
self.peptide_plus_5 = io.LoadEntity("testfiles/peptide_plus_5.pdb")
self.peptide_random = io.LoadEntity("testfiles/peptide_random.pdb")
self.peptide_del_1_2 = io.LoadEntity("testfiles/peptide_del_1_2.pdb")
self.peptide_del_4 = io.LoadEntity("testfiles/peptide_del_4.pdb")
self.peptide_mutation_3 = io.LoadEntity("testfiles/peptide_mutation_3.pdb")
def testRenumbersChainsBasedOnSequence(self):
aln_seq = seq.CreateSequence('A', 'MP-T---NA')
aln_seq.AttachView(self.peptide_original.Select(''))
renumbered = renumber.Renumber(aln_seq)
res = renumbered.residues
self.assertEqual(len(res), 5)
self.assertEqual(res[0].number, 1)
self.assertEqual(res[1].number, 2)
self.assertEqual(res[2].number, 4)
self.assertEqual(res[3].number, 8)
self.assertEqual(res[4].number, 9)
def testRenumbersChainsBasedOnAlignment(self):
aln_seq = seq.CreateSequence('A', 'MP-T---NA')
aln_seq.AttachView(self.peptide_original.Select(''))
aln = seq.CreateAlignment(seq.CreateSequence('A', 'MP-T-XXNA'), aln_seq)
renumbered = renumber.Renumber(aln)
res = renumbered.residues
self.assertEqual(len(res), 5)
self.assertEqual(res[0].number, 1)
self.assertEqual(res[1].number, 2)
self.assertEqual(res[2].number, 4)
self.assertEqual(res[3].number, 8)
self.assertEqual(res[4].number, 9)
def testRenumberPreservesBonds(self):
aln_seq = seq.CreateSequence('A', 'MP-T---NA')
aln_seq.AttachView(self.peptide_original.Select(''))
renumbered = renumber.Renumber(aln_seq)
self.assertTrue(mol.BondExists(renumbered.chains[0].FindAtom(1, 'N'),
renumbered.chains[0].FindAtom(1, 'CA')))
def testClustalWPeptidePlusFive(self):
"""
All residue numbers shifted by 5.
Check whether internal atom order changes while renumbering
(a new entity is generated in the edit_mode)
TODO: add more basic tests: are all properties preserved?
"""
if not clustalw_path:
return
model_seq=seq.SequenceFromChain(" ", self.peptide_plus_5.chains[0])
model_seq.name="model"
aln=ClustalW(self.target_seq,model_seq)
aln.AttachView(1,self.peptide_plus_5.Select(""))
ent_n=renumber.Renumber(aln)
for r_counter in range(len(self.peptide_original.residues)):
assert self.peptide_original.residues[r_counter].qualified_name == ent_n.residues[r_counter].qualified_name, \
"Renumbering failed on residue level: restoring from ResNum+5"
for atom_nr in range(len(self.peptide_original.residues[r_counter].atoms)):
assert self.peptide_original.residues[r_counter].atoms[atom_nr].name==ent_n.residues[r_counter].atoms[atom_nr].name, \
"Renumbering failed on atom level: restoring from ResNum+5"
def testClustalWPeptideRandom(self):
"""
Change residue names in random order
"""
if not clustalw_path:
return
model_seq=seq.SequenceFromChain(" ", self.peptide_random.chains[0])
model_seq.name="model"
aln=ClustalW(self.target_seq,model_seq)
aln.AttachView(1,self.peptide_random.Select(""))
ent_n=renumber.Renumber(aln)
for r_counter in range(len(self.peptide_original.residues)):
assert self.peptide_original.residues[r_counter].qualified_name == ent_n.residues[r_counter].qualified_name, \
"Renumbering failed on residue level: restoring from random residue numbers"
for atom_nr in range(len(self.peptide_original.residues[r_counter].atoms)):
assert self.peptide_original.residues[r_counter].atoms[atom_nr].name==ent_n.residues[r_counter].atoms[atom_nr].name, \
"Renumbering failed on atom level: restoring from random residue numbers"
def testClustalWPeptideDel_1_2(self):
"""
First two residues were removed
"""
if not clustalw_path:
return
model_seq=seq.SequenceFromChain(" ", self.peptide_del_1_2.chains[0])
model_seq.name="model"
aln=ClustalW(self.target_seq,model_seq)
aln.AttachView(1,self.peptide_del_1_2.Select(""))
ent_n=renumber.Renumber(aln)
for r_counter in range(len(self.peptide_original.residues)):
if r_counter==0 or r_counter==1:
continue
assert self.peptide_original.residues[r_counter].qualified_name == ent_n.residues[r_counter-2].qualified_name, \
"Renumbering failed on residue level: restoring from random residue numbers"
for atom_nr in range(len(self.peptide_original.residues[r_counter].atoms)):
assert self.peptide_original.residues[r_counter].atoms[atom_nr].name==ent_n.residues[r_counter-2].atoms[atom_nr].name, \
"Renumbering failed on atom level: restoring from random residue numbers"
def testClustalWPeptideDel_4(self):
"""
Residues in the middle (position 4) was removed
"""
if not clustalw_path:
return
model_seq=seq.SequenceFromChain(" ", self.peptide_del_4.chains[0])
model_seq.name="model"
aln=ClustalW(self.target_seq,model_seq)
aln.AttachView(1,self.peptide_del_4.Select(""))
ent_n=renumber.Renumber(aln)
flag=0
for r_counter in range(len(self.peptide_original.residues)):
if r_counter==3:
flag=1
continue
assert self.peptide_original.residues[r_counter].qualified_name == ent_n.residues[r_counter-flag].qualified_name, \
"Renumbering failed on residue level: restoring from random residue numbers"
for atom_nr in range(len(self.peptide_original.residues[r_counter].atoms)):
assert self.peptide_original.residues[r_counter].atoms[atom_nr].name==ent_n.residues[r_counter-flag].atoms[atom_nr].name, \
"Renumbering failed on atom level: restoring from random residue numbers"
def testClustalWPeptideMutation_3(self):
"""
Mutation to GLY at postion 3
"""
if not clustalw_path:
return
model_seq=seq.SequenceFromChain(" ", self.peptide_mutation_3.chains[0])
model_seq.name="model"
aln=ClustalW(self.target_seq,model_seq)
aln.AttachView(1,self.peptide_mutation_3.Select(""))
self.assertRaises(RuntimeError, renumber.Renumber, aln)
if __name__ == "__main__":
# test renumbering
# test if clustalw package is available on system, otherwise ignore tests
if not clustalw_path:
print("Could not find clustalw executable: ignoring some renumber unit tests")
from ost import testutils
testutils.RunTests()
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