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import unittest
from ost import *
from ost import settings
from ost import seq
def fixture():
e=mol.CreateEntity()
ede=e.EditXCS()
chain=ede.InsertChain('A')
for res in 'ABCDEFGH':
r=ede.AppendResidue(chain, res)
r.SetOneLetterCode(res)
ede.InsertAtom(r, "XXX", geom.Vec3())
return e
class TestSeq(unittest.TestCase):
def setUp(self):
self.ent=fixture()
def testSeqSlice(self):
seq_string='abcdefg'
s=seq.CreateSequence('A', seq_string)
self.assertEqual(s[1:5], seq_string[1:5])
self.assertEqual(s[:-1], seq_string[:-1])
self.assertEqual(s[-3:-2], seq_string[-3:-2])
self.assertEqual(s[-3:], seq_string[-3:])
self.assertEqual(s[3:4], seq_string[3:4])
def testSeqListSlice(self):
a=seq.CreateSequence('A','aaaa')
b=seq.CreateSequence('B','bbbb')
c=seq.CreateSequence('C','cccc')
d=seq.CreateSequence('D','dddd')
sl=seq.CreateSequenceList(a, b, c, d)
sliced=sl[1:]
self.assertEqual(len(sliced), 3)
self.assertEqual(str(sliced[0]), str(b))
self.assertEqual(str(sliced[1]), str(c))
self.assertEqual(str(sliced[2]), str(d))
sliced=sl[:-1]
self.assertEqual(len(sliced), 3)
self.assertEqual(str(sliced[0]), str(a))
self.assertEqual(str(sliced[1]), str(b))
self.assertEqual(str(sliced[2]), str(c))
sliced=sl[-1:]
self.assertEqual(len(sliced), 1)
self.assertEqual(str(sliced[0]), str(d))
def testAlnSlice(self):
a=seq.CreateSequence('A','abcd')
b=seq.CreateSequence('B','efgh')
c=seq.CreateSequence('C','ijkl')
d=seq.CreateSequence('D','mnop')
aln=seq.CreateAlignment(a, b, c, d)
sliced=aln[1:]
self.assertEqual(len(sliced), 3)
self.assertEqual(str(sliced[0]), 'bfjn')
self.assertEqual(str(sliced[1]), 'cgko')
self.assertEqual(str(sliced[2]), 'dhlp')
sliced=aln[:-1]
self.assertEqual(len(sliced), 3)
self.assertEqual(str(sliced[0]), 'aeim')
self.assertEqual(str(sliced[1]), 'bfjn')
self.assertEqual(str(sliced[2]), 'cgko')
sliced=aln[-1:]
self.assertEqual(len(sliced), 1)
self.assertEqual(str(sliced[0]), 'dhlp')
def testViewsFromSequences_01(self):
seq_a=seq.CreateSequence("A", "ABCD-FGH")
seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
seq_b=seq.CreateSequence("B", "ABCDEFGH")
seq_b.AttachView(self.ent.Select(''))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'ABCDFGH')
self.assertEqual(string_b, 'ABCDFGH')
def testSeqIterBZDNG148(self):
s=seq.CreateSequence('A', 'abcdef')
for x in s:
pass
def testViewsFromSequences_02(self):
seq_a=seq.CreateSequence("A", "ABCD-FGH")
seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
seq_b=seq.CreateSequence("B", "ABCD-FGH")
seq_b.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'ABCDFGH')
self.assertEqual(string_b, 'ABCDFGH')
def testViewsFromSequences_03(self):
seq_a=seq.CreateSequence("A", "ABCD--GH")
seq_a.AttachView(self.ent.Select('rname=A,B,C,D,G,H'))
seq_b=seq.CreateSequence("B", "ABCD-FGH")
seq_b.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'ABCDGH')
self.assertEqual(string_b, 'ABCDGH')
def testViewsFromSequences_04(self):
seq_a=seq.CreateSequence("A", "ABCD-FGH")
seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
seq_b=seq.CreateSequence("B", "ABCD--GH")
seq_b.AttachView(self.ent.Select('rname=A,B,C,D,G,H'))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'ABCDGH')
self.assertEqual(string_b, 'ABCDGH')
def testViewsFromSequences_05(self):
seq_a=seq.CreateSequence("A", "ABCD-F--")
seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F'))
seq_b=seq.CreateSequence("B", "ABCDEFGH")
seq_b.AttachView(self.ent.Select('rname=A,B,C,D,E,F,G,H'))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'ABCDF')
self.assertEqual(string_b, 'ABCDF')
def testViewsFromSequences_06(self):
seq_a=seq.CreateSequence("A", "--CD-FGH")
seq_a.AttachView(self.ent.Select('rname=C,D,F,G,H'))
seq_b=seq.CreateSequence("B", "ABCDEFGH")
seq_b.AttachView(self.ent.Select('rname=A,B,C,D,E,F,G,H'))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'CDFGH')
self.assertEqual(string_b, 'CDFGH')
def testViewsFromSequences_07(self):
seq_a=seq.CreateSequence("A", "AB-D-FGH")
seq_a.AttachView(self.ent.Select('rname=A,B,D,F,G,H'))
seq_b=seq.CreateSequence("B", "AB-DEF-H")
seq_b.AttachView(self.ent.Select('rname=A,B,D,E,F,H'))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'ABDFH')
self.assertEqual(string_b, 'ABDFH')
def testViewsFromSequences_08(self):
seq_a=seq.CreateSequence("A", "A-C-E-G")
seq_a.AttachView(self.ent.Select('rname=A,C,E,G'))
seq_b=seq.CreateSequence("B", "-B-D-H-")
seq_b.AttachView(self.ent.Select('rname=B,D,H'))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, '')
self.assertEqual(string_b, '')
def testViewsFromSequences_09(self):
seq_a=seq.CreateSequence("A", "B-D-FGH")
seq_a.AttachView(self.ent.Select('rname=A,B,D,F,G,H'))
seq_a.offset=1
seq_b=seq.CreateSequence("B", "B-DEF-H")
seq_b.offset=1
seq_b.AttachView(self.ent.Select('rname=A,B,D,E,F,H'))
a, b=seq.ViewsFromSequences(seq_a, seq_b)
string_a=''.join([r.one_letter_code for r in a.residues])
string_b=''.join([r.one_letter_code for r in b.residues])
self.assertEqual(string_a, 'BDFH')
self.assertEqual(string_b, 'BDFH')
def testNormalise(self):
seq_a=seq.CreateSequence("A", "B-D-FGH")
self.assertEqual("B-D-FGH", seq_a.GetString())
seq_a.Normalise()
self.assertEqual("BDFGH", seq_a.GetString())
seq_a=seq.CreateSequence("A", "b.d-fgh")
self.assertEqual("b.d-fgh", seq_a.GetString())
seq_a.Normalise()
self.assertEqual("BDFGH", seq_a.GetString())
if __name__== '__main__':
from ost import testutils
testutils.RunTests()
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