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import sys
import unittest
from ost import *
from ost import settings
from ost.bindings import clustalw
class TestClustalWBindings(unittest.TestCase):
def setUp(self):
self.protein = io.LoadEntity("testfiles/testprotein.pdb").Select("cname=A")
self.targetseq = io.LoadSequence("testfiles/test.fasta")
self.targetseq.AttachView(self.protein)
self.templseq = io.LoadSequence("testfiles/similar.fasta")
self.multseq = io.LoadSequenceList("testfiles/multiple.fasta")
self.pw_alignment = io.LoadAlignment("testfiles/pairwise_aln.fasta")
self.nopgap_pw_alignment = io.LoadAlignment("testfiles/nopgap_pairwise_aln.fasta")
self.mult_alignment = io.LoadAlignment("testfiles/multiple_aln.fasta")
self.strseq1 = self.targetseq.GetGaplessString()
self.strseq2 = self.templseq.GetGaplessString()
self.seq1 = io.LoadSequence("testfiles/seq1.fasta")
self.seq2 = io.LoadSequence("testfiles/seq2.fasta")
self.seq1_seq2_alignment = io.LoadAlignment("testfiles/seq1_seq2_aln.fasta")
self.seq1_seq2_alignment_options_changed = io.LoadAlignment("testfiles/seq1_seq2_aln_options_changed.fasta")
def testPairwiseClustalW(self):
aln=clustalw.ClustalW(self.targetseq, self.templseq)
assert self.pw_alignment.ToString(80) == aln.ToString(80), \
"Pairwise alignment differs from precomputed one"
def testNoPGapPariwiseClustalW(self):
aln=clustalw.ClustalW(self.targetseq, self.templseq, nopgap=True)
assert self.nopgap_pw_alignment.ToString(80) == aln.ToString(80), \
"NoPGap pairwise alignment differs from precomputed one"
def testAttachedViewClustalW(self):
aln=clustalw.ClustalW(self.targetseq, self.templseq)
assert aln.FindSequence("testseq").HasAttachedView(), \
"Aligned sequence doesn't have an attached view"
def testMultipleClustalW(self):
aln=clustalw.ClustalW(self.multseq)
# order of sequences in aln may differ (reported by Andrius Merkys who
# found architecture dependent behaviour)
# We therefore check for matching sequence names and respective sequences
# but not for order.
ref_sequences = {s.GetName(): str(s) for s in self.mult_alignment.sequences}
sequences = {s.GetName(): str(s) for s in aln.sequences}
self.assertEqual(sorted(ref_sequences.keys()), sorted(sequences.keys()))
for sname, s in ref_sequences.items():
self.assertEqual(s, sequences[sname])
def testStringClustalW(self):
aln=clustalw.ClustalW(self.strseq1, self.strseq2)
aln.SetSequenceName(0,self.targetseq.GetName())
aln.SetSequenceName(1,self.templseq.GetName())
assert self.pw_alignment.ToString(80) == aln.ToString(80), \
"Pairwise alignment using two strings differs from precomputed one \n%s \n%s" \
%(self.pw_alignment.ToString(80),aln.ToString(80))
def testPairwiseClustalWChangedOptions(self):
# five residues removed two positions before the end of seq2
aln=clustalw.ClustalW(self.seq1,self.seq2)
assert self.seq1_seq2_alignment.ToString(80) == aln.ToString(80), \
"Pairwise alignment with default gap penalties differs from precomputed one"
aln=clustalw.ClustalW(self.seq1,self.seq2,clustalw_option_string="-GAPOPEN=2 -GAPEXT=0")
assert self.seq1_seq2_alignment_options_changed.ToString(80) == aln.ToString(80), \
"Pairwise alignment with modified gap penalties differs from precomputed one"
def testUniqueIdentifier(self):
# common case
seq1 = seq.CreateSequence('heelloo', 'AWESOME')
seq2 = seq.CreateSequence('heelloo', 'AWESOME')
self.assertRaises(ValueError, clustalw.ClustalW, seq1, seq2)
# nasty case with spaces
seq2 = seq.CreateSequence('heelloo dear', 'AWESOME')
self.assertRaises(ValueError, clustalw.ClustalW, seq1, seq2)
if __name__ == "__main__":
# test if clustalw package is available on system, otherwise ignore tests
try:
clustalw_path=settings.Locate(('clustalw', 'clustalw2'))
except(settings.FileNotFound):
print("Could not find clustalw executable: ignoring unit tests")
sys.exit(0)
from ost import testutils
testutils.RunTests()
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