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test_clustalw.py
Studer Gabriel authored
This commit doesn't make OpenStructure work with Python 3. The goal of this commit was to perform an automated port of the Python code and make it compile. The performed steps: - Edited CMakeLists.txt to search for Python with 3.6 as min version 3.6 is the Python version shipped by default with Ubuntu 18.04 LTS - Add version 3.6 to cmake_support/FindPython.cmake - Adapt setup_boost macro in cmake_support/OST.cmake to prefer versioned libraries and not first check for boost_python.so. In the example of Ubuntu 18.04, libboost_python.so is specific for Python 2 but libboost_python3.so is the one we want. - apply the following command: 2to3-2.7 -n -w <OST_DIR> - adapt base/pymod/wrap_base.cc, gui/pymod/wrap_gui.cc and gui/pymod/export_message_widget.cc as PyString functionalities do not exist anymore in the Python 3 interpreter (replaced by PyUnicode) - adapt gui/src/python_shell/python_interpreter_worker.hh to resolve issue discussed in https://stackoverflow.com/questions/23068700/embedding-python3-in-qt-5 Long story short: Qt does a typedef for "slots" which causes trouble with other headers that are pulled in from the Python interpreter
test_clustalw.py 3.66 KiB
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)
assert self.mult_alignment.ToString(80) == aln.ToString(80), \
"Multiple alignment differs from precomputed one"
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()