def test_parse_aminoacid():
pth = os.path.join(MISC_PATH, 'raxml_aminoacid.output')
c = Configuration().init(datatype='protein', phylogeny_program="raxml")
p = raxml.Parser(c)
res = p.parse(open(pth).read())
expected = numpy.array([
0.046704, 0.017460, 0.068093, 0.030991, 0.003492, 0.021388, 0.027499,
0.064164, 0.027499, 0.131820, 0.121781, 0.019642, 0.061545, 0.073330,
0.035356, 0.102139, 0.048014, 0.025753, 0.035356, 0.037975
])
assert numpy.allclose(res.freqs[0], expected)
def test_parse_nucleotide():
pth = os.path.join(MISC_PATH, 'raxml_nucleotide.output')
c = Configuration().init(datatype='DNA', phylogeny_program="raxml")
p = raxml.Parser(c)
res = p.parse(open(pth).read())
expected = numpy.array([
0.315909,
0.232955,
0.190909,
0.260227,
])
assert numpy.allclose(res.freqs[0], expected)
def test_parse_lg4m():
pth = os.path.join(MISC_PATH, 'raxml_aminoacid_LG4M+G.output')
c = Configuration().init(datatype='protein', phylogeny_program="raxml")
p = raxml.Parser(c)
res = p.parse(open(pth).read())
# Make sure we got the first block of rates
expected = numpy.array([
0.082276, 0.055172, 0.043853, 0.053484, 0.018957, 0.028152, 0.046679,
0.15781701, 0.033297, 0.028284, 0.054284, 0.025275, 0.023665, 0.041874,
0.063071, 0.066501, 0.065424, 0.023837, 0.038633, 0.049465
])
assert numpy.allclose(res.freqs[0], expected)
def test_parse_aminoacid():
pth = os.path.join(MISC_PATH, 'raxml_aminoacid.output')
p = raxml.Parser('protein')
p.parse(open(pth).read())
def test_parse_nucleotide():
pth = os.path.join(MISC_PATH, 'raxml_nucleotide.output')
p = raxml.Parser('DNA')
p.parse(open(pth).read())