def test_parse_clustal2_newline(self):
# Bug regession test. Clustal barfed on windows line endings, sometimes
f = data_stream("clustalw2.aln")
s = f.read()
import re
s = re.sub("\n", "\r\n", s) # Change to windows line endings
clustal_io.read(StringIO(s))
f.close()
def test_write(self):
f = StringIO(clustal_io.example)
seqs = clustal_io.read(f)
fout = StringIO()
clustal_io.write(fout, seqs)
fout.seek(0)
seqs2 = clustal_io.read(fout)
self.assertEqual(seqs, seqs2)
f.close()
def test_parse_headerless(self):
f = data_stream("clustal_headerless.aln")
seqs = clustal_io.read(f)
self.assertEqual(len(seqs), 21)
self.assertEqual(seqs[2].name, "O16386_CAEEL")
self.assertEqual(len(seqs[1]), 137)
f.close()
def test_parse_clustal(self):
f = data_stream("clustal.aln")
seqs = clustal_io.read(f)
self.assertEqual(len(seqs), 7)
self.assertEqual(seqs[1].name, "CATH_HUMAN")
self.assertEqual(len(seqs[1]), 395)
f.close()
def test_parse_clustal_example(self):
f = StringIO(clustal_io.example)
clustal_io.read(f)
f.close()
def test_parse_clustalw182(self):
f = data_stream("clustalw182.aln")
clustal_io.read(f, protein_alphabet)
f.close()
def test_parse_clustal_glualign(self):
f = data_stream("clustal_glualign.aln")
clustal_io.read(f, nucleic_alphabet)
f.close()
def test_parse_clustal181(self):
f = data_stream("clustal181.aln")
clustal_io.read(f)
f.close()