def test_correct(self):
lin = rdp.FixrankLineage([['domain', 'D', 1.0], ['phylum', 'P', 1.0],
['class', 'C', 0.75], ['order', 'O', 1.0],
['family', 'F', 1.0], ['genus', 'G', 1.0]])
lin.trim_at_rank('phylum')
assert lin == rdp.FixrankLineage([['domain', 'D', 1.0],
['phylum', 'P', 1.0]])
def test_correct(self):
line = 'seq494517;size=2;\t\tBacteria\tdomain\t1.0\t"Proteobacteria"\tphylum\t1.0\tAlphaproteobacteria\tclass\t0.89\tCaulobacterales\torder\t0.42\tCaulobacteraceae\tfamily\t0.41\tBrevundimonas\tgenus\t0.38\n'
sid, lin = rdp.FixrankParser.parse_line(line)
assert sid == 'seq494517'
assert lin == rdp.FixrankLineage(
[['domain', 'Bacteria', 1.0], ['phylum', 'Proteobacteria', 1.0],
['class', 'Alphaproteobacteria', 0.89],
['order', 'Caulobacterales', 0.42],
['family', 'Caulobacteraceae', 0.41],
['genus', 'Brevundimonas', 0.38]])
class WithEntries:
entries = [
'seq1;size=272905;', '', 'Bacteria', 'domain', '1.0',
'"Bacteroidetes"', 'phylum', '1.0', 'Flavobacteriia', 'class', '0.75',
'"Flavobacteriales"', 'order', '1.0', 'Flavobacteriaceae', 'family',
'1.0', 'Flavobacterium', 'genus', '1.0'
]
sid = 'seq1'
lin = rdp.FixrankLineage([['domain', 'Bacteria', 1.0],
['phylum', 'Bacteroidetes', 1.0],
['class', 'Flavobacteriia', 0.75],
['order', 'Flavobacteriales', 1.0],
['family', 'Flavobacteriaceae', 1.0],
['genus', 'Flavobacterium', 1.0]])
class WithLineage:
lin = rdp.FixrankLineage([['domain', 'Bacteria', 1.0],
['phylum', 'P', 1.0]])
def test_different_lengths(self):
lin1 = rdp.FixrankLineage([['domain', 'Bacteria', 1.0],
['phylum', 'P', 1.0]])
lin2 = rdp.FixrankLineage([['domain', 'Bacteria', 1.0]])
assert lin1 != lin2
def test_different_info(self):
lin1 = rdp.FixrankLineage([['domain', 'Bacteria', 1.0],
['phylum', 'P', 1.0]])
lin2 = rdp.FixrankLineage([['domain', 'Bacteria', 1.0],
['phylum', 'something_else', 1.0]])
assert lin1 != lin2
def test_correct(self):
lin1 = rdp.FixrankLineage([['domain', 'Bacteria', 1.0],
['phylum', 'P', 1.0]])
lin2 = rdp.FixrankLineage([['domain', 'Bacteria', 1.0],
['phylum', 'P', 1.0]])
assert lin1 == lin2
def test_correct(self):
assert self.lin.ranks_at_confidence(0.8) == rdp.FixrankLineage(
[['domain', 'Bacteria', 1.0], ['phylum', 'Bacteroidetes',
1.0]]).ranks