def split(self, split_by="123"):
"""Splits a MSA and returns a dictionary of keys to MSAs,
using the keys in the 'split_by' parameter at the top
level. See also paleomix.common.sequences.split."""
self.validate(self)
if not split_by:
raise TypeError("No partitions to split by specified")
results = dict((key, set()) for key in split_by)
for record in self:
for (key, partition) in split(record.sequence, split_by).items():
results[key].add(FASTA(record.name, None, partition))
for (key, value) in results.items():
results[key] = MSA(value)
return results
def split(self, split_by = "123"):
"""Splits a MSA and returns a dictionary of keys to MSAs,
using the keys in the 'split_by' parameter at the top
level. See also paleomix.common.sequences.split."""
self.validate(self)
if not split_by:
raise TypeError("No partitions to split by specified")
results = dict((key, set()) for key in split_by)
for record in self:
for (key, partition) in split(record.sequence, split_by).iteritems():
results[key].add(FASTA(record.name, None, partition))
for (key, value) in results.items():
results[key] = MSA(value)
return results
def test_split__empty_sequence():
assert_equal(split(""), {"1": "", "2": "", "3": ""})
def test_split__partial_group():
expected = {"1": "AA", "2": "CA", "3": "G"}
assert split("ACGAA") == expected
def test_split__empty_group():
expected = {"1": "A", "2": "C", "3": ""}
assert split("AC") == expected
def test_split__no_split_by():
split("", split_by="")
def test_split__empty_group():
expected = {"1": "A", "2": "C", "3": ""}
assert_equal(split("AC"), expected)
def test_split__two_groups():
assert_equal(split("ACGCAT", "112"), {"1": "ACCA", "2": "GT"})
def test_split__empty_sequence():
assert split("") == {"1": "", "2": "", "3": ""}
def test_split__partial_group():
expected = {"1": "AA", "2": "CA", "3": "G"}
assert_equal(split("ACGAA"), expected)
def test_split__empty_group():
expected = {"1": "A", "2": "C", "3": ""}
assert_equal(split("AC"), expected)
def test_split__three_groups():
expected = {"1": "AC", "2": "CA", "3": "GT"}
assert_equal(split("ACGCAT", "123"), expected)
assert_equal(split("ACGCAT"), expected)
def test_split__two_groups():
assert_equal(split("ACGCAT", "112"), {"1": "ACCA", "2": "GT"})
def test_split__single_group():
assert_equal(split("ACGCAT", "111"), {'1': 'ACGCAT'})
def test_split__no_split_by():
split("", split_by="")
def test_split__single_group():
assert_equal(split("ACGCAT", "111"), {'1': 'ACGCAT'})
def test_split__no_split_by():
with pytest.raises(ValueError, match="No split_by specified"):
split("", split_by="")
def test_split__three_groups():
expected = {"1": "AC", "2": "CA", "3": "GT"}
assert_equal(split("ACGCAT", "123"), expected)
assert_equal(split("ACGCAT"), expected)
def test_split__single_group():
assert split("ACGCAT", "111") == {"1": "ACGCAT"}
def test_split__partial_group():
expected = {"1": "AA", "2": "CA", "3": "G"}
assert_equal(split("ACGAA"), expected)
def test_split__two_groups():
assert split("ACGCAT", "112") == {"1": "ACCA", "2": "GT"}
def test_split__three_groups():
expected = {"1": "AC", "2": "CA", "3": "GT"}
assert split("ACGCAT", "123") == expected
assert split("ACGCAT") == expected
def test_split__empty_sequence():
assert_equal(split(""), {"1": "", "2": "", "3": ""})