def test_find_lca_2():
tree = build_tree([[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2a')],
[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2b')],
])
lca = find_lca(tree)
assert lca == ((LineagePair('rank1', 'name1'),), 2)
def test_build_tree():
tree = build_tree(
[[LineagePair('rank1', 'name1'),
LineagePair('rank2', 'name2')]])
assert tree == {
LineagePair('rank1', 'name1'): {
LineagePair('rank2', 'name2'): {}
}
}
def test_find_lca():
tree = build_tree(
[[LineagePair('rank1', 'name1'),
LineagePair('rank2', 'name2')]])
lca = find_lca(tree)
assert lca == ((
LineagePair('rank1', 'name1'),
LineagePair('rank2', 'name2'),
), 0)
def load_taxonomy_assignments(filename,
delimiter=',',
start_column=2,
use_headers=True,
force=False):
# parse spreadsheet!
fp = open(filename, 'rtU')
r = csv.reader(fp, delimiter=delimiter)
row_headers = ['identifiers']
row_headers += ['_skip_'] * (start_column - 2)
row_headers += list(lca_utils.taxlist())
# first check that headers are interpretable.
if use_headers:
notify('examining spreadsheet headers...')
first_row = next(iter(r))
n_disagree = 0
for (column, value) in zip(row_headers, first_row):
if column == '_skip_':
continue
if column.lower() != value.lower():
notify("** assuming column '{}' is {} in spreadsheet", value,
column)
n_disagree += 1
if n_disagree > 2:
error('whoa, too many assumptions. are the headers right?')
error('expecting {}', ",".join(row_headers))
if not force:
sys.exit(-1)
notify('...continue, because --force was specified.')
# convert into a lineage pair
assignments = {}
num_rows = 0
for row in r:
if row and row[0].strip(): # want non-empty row
num_rows += 1
lineage = list(zip(row_headers, row))
lineage = [x for x in lineage if x[0] != '_skip_']
ident = lineage[0][1]
lineage = lineage[1:]
# clean lineage of null names, replace with 'unassigned'
lineage = [(a, lca_utils.filter_null(b)) for (a, b) in lineage]
lineage = [LineagePair(a, b) for (a, b) in lineage]
# remove end nulls
while lineage and lineage[-1].name == 'unassigned':
lineage = lineage[:-1]
# store lineage tuple
if lineage:
assignments[ident] = tuple(lineage)
fp.close()
return assignments, num_rows
def test_build_tree_2():
tree = build_tree([[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2a')],
[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2b')],
])
assert tree == { LineagePair('rank1', 'name1'): { LineagePair('rank2', 'name2a') : {},
LineagePair('rank2', 'name2b') : {}} }
def test_build_tree_3(): # empty 'rank2' name
tree = build_tree(
[[LineagePair('rank1', 'name1'),
LineagePair('rank2', '')]])
assert tree == {LineagePair('rank1', 'name1'): {}}