def test_fasta_from_alignment(self):
"""should return correct fasta string."""
self.assertEqual(fasta_from_alignment({}), '')
self.assertEqual(fasta_from_alignment(self.alignment_dict),
self.fasta_with_label)
self.assertEqual(
fasta_from_alignment(self.alignment_dict, line_wrap=2),
self.fasta_with_label_lw2)
def test_fasta_from_alignment_from_alignment(self):
"""should return correct fasta string for alignment object"""
# alignment with a few sequences
obs = fasta_from_alignment(self.alignment)
self.assertEquals('>seq1\nACC--G-GGTA..\n>seqs2\nTCC--G-GGCA..', obs)
# empty alginment
obs = fasta_from_alignment(Alignment([]))
self.assertEquals('', obs)
# alignment with a few sequences
obs = fasta_from_alignment(self.alignment, sort=False)
self.assertEquals('>seq1\nACC--G-GGTA..\n>seqs2\nTCC--G-GGCA..', obs)
def test_fasta_from_alignment_from_alignment(self):
"""should return correct fasta string for alignment object"""
# alignment with a few sequences
obs = fasta_from_alignment(self.alignment)
self.assertEquals(">seq1\nACC--G-GGTA..\n>seqs2\nTCC--G-GGCA..", obs)
# empty alginment
obs = fasta_from_alignment(Alignment([]))
self.assertEquals("", obs)
# alignment with a few sequences
obs = fasta_from_alignment(self.alignment, sort=False)
self.assertEquals(">seq1\nACC--G-GGTA..\n>seqs2\nTCC--G-GGCA..", obs)
def test_fasta_from_alignment(self):
"""should return correct fasta string."""
self.assertEqual(fasta_from_alignment({}), "")
self.assertEqual(fasta_from_alignment(self.alignment_dict), self.fasta_with_label)
self.assertEqual(fasta_from_alignment(self.alignment_dict, line_wrap=2), self.fasta_with_label_lw2)
