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)