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()