def test_parse_crab(self):
f = data_stream('crab.nbrf')
seqs = nbrf_io.read(f)
self.assertEqual(seqs[0].alphabet, protein_alphabet)
self.assertEqual(len(seqs), 9)
self.assertEqual(seqs[2].name, "CRAB_CHICK")
self.assertEqual(seqs[2].description,
"ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).")
f.close()
def test_pir_file_from_clustal(self):
f = data_stream('clustalw.pir')
seqs = nbrf_io.read(f)
self.assertEqual(len(seqs), 2)
self.assertEqual(
seqs[1].endswith(
'C-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-A----------------------------------------'
'-----------------------------------------'), True)
f.close()
def test_parse_cox2(self):
f = data_stream('cox2.nbrf')
seqs = nbrf_io.read(f)
self.assertEqual(len(seqs), 5)
self.assertEqual(len(seqs[1]), 210)
self.assertEqual(
str(seqs[0]),
"MAFILSFWMIFLLDSVIVLLSFVCFVCVWICALLFSTVLLVSKLNNIYCTWDFTASKFIDVYWFTIGGMFSLG"
"LLLRLCLLLYFGHLNFVSFDLCKVVGFQWYWVYFIFGETTIFSNLILESDYMIGDLRLLQCNHVLTLLSLVIY"
"KLWLSAVDVIHSFAISSLGVKVENLVAVMK")
self.assertEqual(seqs[0].alphabet, protein_alphabet)
f.close()
def test_parse_protein(self):
f = data_stream('protein.pir')
seqs = nbrf_io.read(f)
self.assertEqual(seqs[0].alphabet, protein_alphabet)
self.assertEqual(len(seqs), 10)
f.close()
def test_parse_examples(self):
f = data_stream('rhod.pir')
seqs = nbrf_io.read(f)
self.assertEqual(seqs[0].alphabet, protein_alphabet)
self.assertEqual(len(seqs), 3)
f.close()
def test_parse_dna(self):
f = data_stream('dna.pir')
seqs = nbrf_io.read(f)
self.assertEqual(seqs[0].alphabet, dna_alphabet)
self.assertEqual(len(seqs), 10)
f.close()
