def test_global_revcomp(self):
er = EdlibRunner("global", revcomp=True)
aln = er.align(revcomp_seq(self.y), self.x)
self.assertEqual(aln.strand, 1)
self.assertEqual(aln.cigar, self.cigar_x2y_global.revcomp())
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.b_start, 0)
self.assertEqual(aln.a_end, len(self.y))
self.assertEqual(aln.b_end, len(self.x))
self.assertEqual(aln.a_aligned_seq, revcomp_seq(self.y))
self.assertEqual(aln.b_aligned_seq, revcomp_seq(self.x))
aln = er.align(self.y, revcomp_seq(self.x))
self.assertEqual(aln.strand, 1)
self.assertEqual(aln.cigar, self.cigar_x2y_global)
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.b_start, 0)
self.assertEqual(aln.a_end, len(self.y))
self.assertEqual(aln.b_end, len(self.x))
self.assertEqual(aln.a_aligned_seq, self.y)
self.assertEqual(aln.b_aligned_seq, self.x)
aln = er.align(self.x, revcomp_seq(self.y))
self.assertEqual(aln.strand, 1)
self.assertEqual(aln.cigar, self.cigar_x2y_global.swap())
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.b_start, 0)
self.assertEqual(aln.a_end, len(self.x))
self.assertEqual(aln.b_end, len(self.y))
self.assertEqual(aln.a_aligned_seq, self.x)
self.assertEqual(aln.b_aligned_seq, self.y)
def test_glocal_revcomp(self):
er = EdlibRunner("glocal", revcomp=True)
aln = er.align(revcomp_seq(self.y), self.x)
self.assertEqual(aln.strand, 1)
self.assertEqual(aln.cigar, self.cigar_x2y_glocal.revcomp())
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.b_start, self.x_glocal_start)
self.assertEqual(aln.a_end, len(self.y))
self.assertEqual(aln.b_end, self.x_glocal_end) # position is forward
self.assertEqual(aln.a_aligned_seq, revcomp_seq(self.y))
self.assertEqual(aln.b_aligned_seq,
revcomp_seq(self.x_glocal)) # seq is revcomp
aln = er.align(self.y, revcomp_seq(self.x))
self.assertEqual(aln.strand, 1)
self.assertEqual(aln.cigar, self.cigar_x2y_glocal)
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.b_start, len(self.x) - self.x_glocal_end)
self.assertEqual(aln.a_end, len(self.y))
self.assertEqual(aln.b_end,
len(self.x) - self.x_glocal_start) # rc(x) is forward
self.assertEqual(aln.a_aligned_seq, self.y)
self.assertEqual(aln.b_aligned_seq, self.x_glocal) # seq is forward
# inappropriate use-case (mapped seq is shorter)
aln = er.align(self.x, revcomp_seq(self.y))
self.assertEqual(aln.strand, 1)
self.assertEqual(aln.cigar, self.cigar_x2y_global.swap())
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.b_start, 0)
self.assertEqual(aln.a_end, len(self.x))
self.assertEqual(aln.b_end, len(self.y))
self.assertEqual(aln.a_aligned_seq, self.x)
self.assertEqual(aln.b_aligned_seq, self.y)
def test_global_forward(self):
er = EdlibRunner("global", revcomp=False)
aln = er.align(self.y, self.x)
self.assertEqual(aln.cigar, self.cigar_x2y_global)
self.assertEqual(aln.a_aligned_seq, self.y)
self.assertEqual(aln.b_aligned_seq, self.x)
aln = er.align(self.x, self.y)
self.assertEqual(aln.cigar, self.cigar_x2y_global.swap())
self.assertEqual(aln.a_aligned_seq, self.x)
self.assertEqual(aln.b_aligned_seq, self.y)
def test_prefix(self):
er = EdlibRunner("prefix", revcomp=False)
aln = er.align(self.y, self.x)
self.assertEqual(aln.cigar, self.cigar_x2y_prefix)
self.assertEqual(aln.a_aligned_seq, self.y)
self.assertEqual(aln.b_aligned_seq, self.x_prefix)
# inappropriate use-case (mapped seq is shorter)
aln = er.align(self.x, self.y)
self.assertEqual(aln.cigar, self.cigar_x2y_global.swap())
self.assertEqual(aln.a_aligned_seq, self.x)
self.assertEqual(aln.b_aligned_seq, self.y)
def test_global_forward_cyclic(self):
er = EdlibRunner("global", revcomp=False, cyclic=True)
aln = er.align(self.z, self.x) # z vs xx
self.assertIn(aln.cigar, self.cigar_xx2z)
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.a_end, len(self.z))
self.assertIn(aln.b_start, self.x_cyclic_start)
self.assertEqual(aln.b_start, aln.b_end)
self.assertEqual(aln.a_aligned_seq, self.z)
self.assertIn(aln.b_aligned_seq, self.x_cyclic)
aln = er.align(self.x, self.z) # x vs zz
self.assertIn(aln.cigar, self.cigar_zz2x)
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.a_end, len(self.x))
self.assertIn(aln.b_start, self.z_cyclic_start)
self.assertEqual(aln.b_start, aln.b_end)
self.assertEqual(aln.a_aligned_seq, self.x)
self.assertIn(aln.b_aligned_seq, self.z_cyclic)
def test_global_revcomp_cyclic(self):
er = EdlibRunner("global", revcomp=True, cyclic=True)
aln = er.align(revcomp_seq(self.z), self.x) # rc(z) vs xx
self.assertEqual(aln.strand, 1)
self.assertIn(aln.cigar, [x.revcomp() for x in self.cigar_xx2z])
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.a_end, len(self.z))
self.assertIn(aln.b_start, self.x_cyclic_start)
self.assertEqual(aln.b_start, aln.b_end)
self.assertEqual(aln.a_aligned_seq, revcomp_seq(self.z))
self.assertIn(aln.b_aligned_seq,
[revcomp_seq(x) for x in self.x_cyclic])
aln = er.align(self.z, revcomp_seq(self.x)) # z vs rc(xx)
self.assertEqual(aln.strand, 1)
self.assertIn(aln.cigar, self.cigar_xx2z)
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.a_end, len(self.z))
self.assertIn(aln.b_start,
[len(self.x) - x for x in self.x_cyclic_start])
self.assertEqual(aln.b_start, aln.b_end)
self.assertEqual(aln.a_aligned_seq, self.z)
self.assertIn(aln.b_aligned_seq, self.x_cyclic)
aln = er.align(revcomp_seq(self.x), self.z) # rc(x) vs zz
self.assertEqual(aln.strand, 1)
self.assertIn(aln.cigar, [x.revcomp() for x in self.cigar_zz2x])
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.a_end, len(self.x))
self.assertIn(aln.b_start, self.z_cyclic_start)
self.assertEqual(aln.b_start, aln.b_end)
self.assertEqual(aln.a_aligned_seq, revcomp_seq(self.x))
self.assertIn(aln.b_aligned_seq,
[revcomp_seq(x) for x in self.z_cyclic])
aln = er.align(self.x, revcomp_seq(self.z)) # x vs rc(zz)
self.assertEqual(aln.strand, 1)
self.assertIn(aln.cigar, self.cigar_zz2x)
self.assertEqual(aln.a_start, 0)
self.assertEqual(aln.a_end, len(self.x))
self.assertIn(aln.b_start,
[len(self.z) - x for x in self.z_cyclic_start])
self.assertEqual(aln.b_start, aln.b_end)
self.assertEqual(aln.a_aligned_seq, self.x)
self.assertIn(aln.b_aligned_seq, self.z_cyclic)