def test_read_example_array(self):
f = StringIO(array_io.example)
seqs = seq_io.read(f)
# print seqs
self.assertEqual(len(seqs), 8)
self.assertEqual(seqs[0].name, None)
self.assertEqual(len(seqs[1]), 60)
def test_read_fasta(self):
f = StringIO(fasta_io.example)
seqs = seq_io.read(f)
# print seqs
self.assertEqual(len(seqs), 3)
self.assertEqual(seqs[0].description, "Lamprey GLOBIN V - SEA LAMPREY")
self.assertEqual(len(seqs[1]), 231)
def test_which_alphabet(self):
a = Alphabet.which(Seq("ARNDCQEGHILKMFPSTWYVX"))
assert a == unambiguous_protein_alphabet
f1 = data_stream('cap.fa')
f2 = data_stream('cox2.msf')
f3 = data_stream('Rv3829c.fasta')
f4 = data_stream('chain_B.fasta')
tests = (
(seq_io.read(f1), unambiguous_dna_alphabet),
(seq_io.read(f2), unambiguous_protein_alphabet),
(seq_io.read(f3), unambiguous_protein_alphabet),
(seq_io.read(f4), unambiguous_protein_alphabet),
)
for t in tests:
self.assertEqual(Alphabet.which(t[0]), t[1])
f1.close()
f2.close()
f3.close()
f4.close()
def test_read(self):
f = data_stream("genbank/cox2.gb")
seqs = genbank_io.read(f)
self.assertEqual(len(seqs), 5)
self.assertEqual(len(seqs[1]), 210)
f.seek(0)
seqs = seq_io.read(f)
self.assertEqual(len(seqs), 5)
self.assertEqual(len(seqs[1]), 210)
f.close()
f = data_stream("genbank/NT_019265.gb")
seqs = genbank_io.read(f)
self.assertEqual(len(seqs), 0)
f.close()
def test_parse_globin_fasta(self):
with data_stream("globin.fa") as f:
seqs = seq_io.read(f)
self.assertEqual(len(seqs), 56)
def test_parse_clustalw182(self):
with data_stream("clustalw182.aln") as f:
seq_io.read(f, protein_alphabet)
def test_parse_clustal_glualign(self):
with data_stream("clustal_glualign.aln") as f:
seq_io.read(f, nucleic_alphabet)
def test_parse_clustal(self):
with data_stream("clustal.aln") as f:
seqs = seq_io.read(f)
self.assertEqual(len(seqs), 7)
self.assertEqual(seqs[1].name, "CATH_HUMAN")
self.assertEqual(len(seqs[1]), 395)
