def write_clustal(self, f):
"""
write Clustal alignment to a file
code from Bio.AlingIO.ClustalIO is used
:param f:
:return:
"""
# transform possible unclustal gap characters to dashes
clustalized_alig = self._clustalize_alignment(self)
writer = ClustalWriter(f)
writer.write_alignment(clustalized_alig)
def test_write_read(self):
"""Checking write/read."""
alignments = (list(ClustalIterator(StringIO(aln_example1)))
+ list(ClustalIterator(StringIO(aln_example2))) * 2)
handle = StringIO()
self.assertEqual(3, ClustalWriter(handle).write_file(alignments))
handle.seek(0)
for i, a in enumerate(ClustalIterator(handle)):
self.assertEqual(a.get_alignment_length(), alignments[i].get_alignment_length())
def test_write_read_single(self):
"""Testing write/read when there is only one sequence."""
alignment = next(ClustalIterator(StringIO(aln_example1)))
# Now thae just the first row as a new alignment:
alignment = alignment[0:1]
handle = StringIO()
ClustalWriter(handle).write_file([alignment])
handle.seek(0)
for i, a in enumerate(ClustalIterator(handle)):
self.assertEqual(a.get_alignment_length(), alignment.get_alignment_length())
self.assertEqual(len(a), 1)
