def test_infer_close_group(self):
me = Analyze()
me.taxdump = taxdump_from_text(taxdump_proteo)
add_children(me.taxdump)
me.groups = {}
# close group is parent of LCA of self group
me.self_tax = ['562'] # E. coli
me.groups['self'] = set(['562'] + get_descendants('562', me.taxdump))
me.close_tax = None
me.close_size = None
me.infer_close_group()
self.assertListEqual(me.close_tax, ['561']) # Escherichia
self.assertSetEqual(me.groups['close'], {'561', '2580236'})
# close group must have at least 5 taxa
me.close_tax = None
me.groups['close'] = None
me.close_size = 5
me.infer_close_group()
self.assertListEqual(me.close_tax, ['543']) # Enterobacteriaceae
exp = {'543', '620', '622', '570', '548', '561', '2580236'}
self.assertSetEqual(me.groups['close'], exp)
# close group is LCA of multiple self groups
me.self_tax = ['561', '620'] # Escherichia and Shigella
me.groups['self'] = set().union(*[[x] + get_descendants(x, me.taxdump)
for x in me.self_tax])
me.close_tax = None
me.groups['close'] = None
me.close_size = None
me.infer_close_group()
self.assertListEqual(me.close_tax, ['543']) # Enterobacteriaceae
exp = {'543', '570', '548'}
self.assertSetEqual(me.groups['close'], exp)
def test_define_groups(self):
me = Analyze()
me.taxdump = taxdump_from_text(taxdump_proteo)
add_children(me.taxdump)
me.groups = {}
# user defined groups:
# self: genera Escherichia and Shigella
# close: family Enterobacteriaceae
me.groups = {}
me.self_tax = '561,620'
me.close_tax = '543'
me.define_groups()
self.assertListEqual(me.self_tax, ['561', '620'])
exp = {'561', '562', '585056', '1038927', '2580236', '620', '622'}
self.assertSetEqual(me.groups['self'], exp)
self.assertListEqual(me.close_tax, ['543'])
exp = {'543', '548', '570'}
self.assertSetEqual(me.groups['close'], exp)
# auto-infer groups
me.self_tax = {}
me.close_tax = {}
me.lca = '562' # all inputs are E. coli
me.self_rank = 'genus' # but we want to raise self to genus
me.close_size = 2 # close group must be this big or bigger
me.define_groups()
self.assertListEqual(me.self_tax, ['561'])
exp = {'561', '562', '585056', '1038927', '2580236'}
self.assertSetEqual(me.groups['self'], exp)
self.assertListEqual(me.close_tax, ['543'])
exp = {'543', '548', '570', '620', '622'}
self.assertSetEqual(me.groups['close'], exp)
