def test_tigger(alignment_text):
a = Alignment()
a.parse(alignment_text)
bitsets, slow_rates = slow_tiger(a)
tigger = TigerDNA()
tigger.build_bitsets(a)
fast_rates = tigger.calc_rates()
assert np.allclose(slow_rates, fast_rates)
def test_subset():
a = Alignment()
a.parse(INTERLEAVED)
ss = FakeSubset([0, 1, 5, 7])
b = SubsetAlignment(a, ss)
assert b.sequence_length == len(ss.columns)
for i, c in enumerate(ss.columns):
assert (b.data[:, i] == a.data[:, c]).all()
def test_subset():
a = Alignment()
a.parse(INTERLEAVED)
ss = FakeSubset([0, 1, 5, 7])
b = SubsetAlignment(a, ss)
assert b.sequence_length == len(ss.columns)
for i, c in enumerate(ss.columns):
assert (b.data[:, i] == a.data[:, c]).all()
def test_load_and_save_phy(phyml_path):
a = Alignment()
a.read(phyml_path)
b = Alignment()
b.parse(write_and_get_stream(a))
assert (a.data == b.data).all()
assert a.species == b.species
def test_simple():
a = Alignment()
a.parse(BASIC)
assert a.species_count == 5
assert a.sequence_length == 10
assert a.data.shape == (5, 10)
b = Alignment()
b.parse(write_and_get_stream(a))
assert (a.data == b.data).all()
assert a.species == b.species
def test_load_and_save_phy(phyml_path):
a = Alignment()
a.read(phyml_path)
b = Alignment()
b.parse(write_and_get_stream(a))
assert (a.data == b.data).all()
assert a.species == b.species
def test_simple():
a = Alignment()
a.parse(BASIC)
assert a.species_count == 5
assert a.sequence_length == 10
assert a.data.shape == (5, 10)
b = Alignment()
b.parse(write_and_get_stream(a))
assert (a.data == b.data).all()
assert a.species == b.species
import pytest
import os
from partfinder import morph_tiger
from partfinder.alignment import Alignment
MORPH_DATA = """
5 25
tax1 1101100000111111021200001
tax2 110110010?0011100212?0000
tax3 ?11210?1010?00101000?010?
tax4 1021011201000010111111111
tax5 10?1011311000120121211111
"""
MORPH_ALIGN = Alignment()
MORPH_ALIGN.parse(MORPH_DATA)
def test_set_parts():
set_parts = morph_tiger.create_set_parts(MORPH_ALIGN)
assert set_parts == [
[[0, 1, 3, 4]],
[[3, 4], [0, 1, 2]],
[[0, 1], [2], [3]],
[[0, 1, 3, 4], [2]],
[[3, 4], [0, 1, 2]],
[[0, 1, 2], [3, 4]],
[[0, 1], [3, 4]],
[[0], [1, 2], [3], [4]],
[[0, 1, 2, 3], [4]],
import pytest
import os
from partfinder import morph_tiger
from partfinder.alignment import Alignment
MORPH_DATA = """
5 25
tax1 1101100000111111021200001
tax2 110110010?0011100212?0000
tax3 ?11210?1010?00101000?010?
tax4 1021011201000010111111111
tax5 10?1011311000120121211111
"""
MORPH_ALIGN = Alignment()
MORPH_ALIGN.parse(MORPH_DATA)
def test_set_parts():
set_parts = morph_tiger.create_set_parts(MORPH_ALIGN)
assert set_parts == [[[0, 1, 3, 4]], [[3, 4], [0, 1, 2]],
[[0, 1], [2], [3]], [[0, 1, 3, 4], [2]],
[[3, 4], [0, 1, 2]], [[0, 1, 2], [3, 4]],
[[0, 1], [3, 4]], [[0], [1, 2], [3], [4]],
[[0, 1, 2, 3], [4]], [[0], [2, 3, 4]],
[[1, 2, 3, 4], [0]], [[1, 3, 4], [0]],
[[2, 3, 4], [0, 1]], [[2, 3], [0, 1, 4]],
[[0, 1, 2, 3], [4]], [[1, 2, 3, 4], [0]],
[[0, 1], [2, 3, 4]], [[2], [3], [0, 1, 4]],
[[2], [0, 1, 3, 4]], [[2], [3], [0, 1, 4]],
def test_too_many_species(caplog):
a = Alignment()
with pytest.raises(AlignmentError):
a.parse(TOO_MANY_SPECIES)
assert "Phyml format error" in caplog.text()
def test_too_few_species(caplog):
a = Alignment()
with pytest.raises(AlignmentError):
a.parse(TOO_FEW_SPECIES)
assert "too many species" in caplog.text()
def test_interleaved():
a = Alignment()
a.parse(INTERLEAVED)
assert a.species_count == 5
assert a.sequence_length == 30
assert a.data.shape == (5, 30)
def test_too_many_species(caplog):
a = Alignment()
with pytest.raises(AlignmentError):
a.parse(TOO_MANY_SPECIES)
assert "Phyml format error" in caplog.text()
def test_too_few_species(caplog):
a = Alignment()
with pytest.raises(AlignmentError):
a.parse(TOO_FEW_SPECIES)
assert "too many species" in caplog.text()
def test_interleaved():
a = Alignment()
a.parse(INTERLEAVED)
assert a.species_count == 5
assert a.sequence_length == 30
assert a.data.shape == (5, 30)