def test_which(self):
tests = (
(seq_io.read(testdata_stream('cap.fa')), unambiguous_dna_alphabet),
(seq_io.read(testdata_stream('cox2.msf')), unambiguous_protein_alphabet),
(seq_io.read(testdata_stream('Rv3829c.fasta')), unambiguous_protein_alphabet),
)
for t in tests :
self.failUnlessEqual(which_alphabet(t[0]), t[1])
def test_which_alphabet(self):
a = Alphabet.which(Seq("ARNDCQEGHILKMFPSTWYVX"))
assert a == unambiguous_protein_alphabet
tests = (
(seq_io.read(testdata_stream('cap.fa')), unambiguous_dna_alphabet),
(seq_io.read(testdata_stream('cox2.msf')), unambiguous_protein_alphabet),
(seq_io.read(testdata_stream('Rv3829c.fasta')), unambiguous_protein_alphabet),
(seq_io.read(testdata_stream('chain_B.fasta')), unambiguous_protein_alphabet),
)
for t in tests :
self.failUnlessEqual(Alphabet.which(t[0]), t[1])
def test_which_alphabet(self):
a = Alphabet.which(Seq("ARNDCQEGHILKMFPSTWYVX"))
assert a == unambiguous_protein_alphabet
tests = (
(seq_io.read(testdata_stream('cap.fa')), unambiguous_dna_alphabet),
(seq_io.read(testdata_stream('cox2.msf')),
unambiguous_protein_alphabet),
(seq_io.read(testdata_stream('Rv3829c.fasta')),
unambiguous_protein_alphabet),
)
for t in tests:
self.failUnlessEqual(Alphabet.which(t[0]), t[1])
def test_which_alphabet(self):
a = Alphabet.which(Seq("ARNDCQEGHILKMFPSTWYVX"))
assert a == unambiguous_protein_alphabet
f1=testdata_stream('cap.fa')
f2=testdata_stream('cox2.msf')
f3=testdata_stream('Rv3829c.fasta')
f4=testdata_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_which_alphabet(self):
a = Alphabet.which(Seq("ARNDCQEGHILKMFPSTWYVX"))
assert a == unambiguous_protein_alphabet
f1 = testdata_stream('cap.fa')
f2 = testdata_stream('cox2.msf')
f3 = testdata_stream('Rv3829c.fasta')
f4 = testdata_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 = testdata_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 = testdata_stream('genbank/NT_019265.gb')
seqs = genbank_io.read(f)
self.assertEqual(len(seqs), 0)
f.close()