def test_distance_matrix(self):
"""distance_matrix should obey RowOrder of alignment"""
#RowOrder=None
aln1_exp = array([[0,2,2],[2,0,1],[2,1,0]])
self.assertEqual(distance_matrix(self.aln1),aln1_exp)
a = Alignment(self.aln1.copy())
a.RowOrder=[1,2,0]
a_exp = array([[0,1,2],[1,0,2],[2,2,0]])
self.assertEqual(distance_matrix(a),a_exp)
def ClustalParser(record, seq_constructor=Sequence, strict=True):
"""Returns contents of record as Alignment object."""
seqs, label_order = MinimalClustalParser(record, strict)
result = Alignment()
for label, seq in seqs.items():
new_seq = seq_constructor(''.join(map(strip, seq)))
try:
new_seq.Label = label
except AttributeError:
pass
result[label] = new_seq
result.RowOrder = label_order
return result
