def test_find_match(self):
me = Analyze()
me.taxdump = taxdump_from_text(taxdump_proteo)
add_children(me.taxdump)
df = pd.DataFrame(
[
[100, '585056'], # E. coli UMN026
[99, '1038927'], # E. coli O104:H4
[97, '562'], # Escherichia coli
[95, '622'], # Shigella dysenteriae
[92, '543'], # Enterobacteriaceae
[88, '548'], # Klebsiella aerogenes
[80, '766']
], # Rickettsiales
columns=['score', 'taxid'])
# keep top 1% hits
me.match_th = 0.99
self.assertEqual(me.find_match(df), '562')
# keep top 10% hits
me.match_th = 0.9
self.assertEqual(me.find_match(df), '543')
# keep top 20% hits
me.match_th = 0.8
self.assertEqual(me.find_match(df), '1224')
# input DataFrame is empty
self.assertEqual(me.find_match(pd.DataFrame()), '0')
def test_calc_scores(self):
columns = ('id', 'taxid', 'score')
# helper for making hit table
def _hits_df(data):
return pd.DataFrame(data, columns=columns).set_index('id')
me = Analyze()
me.taxdump = taxdump_from_text(taxdump_proteo)
add_children(me.taxdump)
me.groups = {
'self': {'561', '562', '585056'},
'close': {'543', '91347', '1236'}
}
me.data = {
'S1': [{
'score': 100,
'hits': _hits_df((('P1', '561', 100), ('P2', '562', 95)))
}, {
'score': 90,
'hits': _hits_df((('P3', '561', 81), ('P4', '543', 72)))
}],
'S2': [{
'score':
96,
'hits':
_hits_df(
(('P5', '561', 90), ('P6', '543', 84), ('P7', '620', 66)))
}]
}
me.weighted = True
me.match_th = 0.9
me.calc_scores()
# helper for get scores
def _prot_scores(prot):
return [prot[x] for x in ('self', 'close', 'distal')]
s1_1 = me.data['S1'][0]
self.assertListEqual(s1_1['hits']['group'].tolist(), ['self', 'self'])
self.assertListEqual(_prot_scores(s1_1), [1.95, 0.0, 0.0])
self.assertEqual(s1_1['match'], '0')
s1_2 = me.data['S1'][1]
self.assertListEqual(s1_2['hits']['group'].tolist(), ['self', 'close'])
self.assertListEqual(_prot_scores(s1_2), [0.9, 0.8, 0.0])
self.assertEqual(s1_2['match'], '0')
s2_1 = me.data['S2'][0]
self.assertListEqual(s2_1['hits']['group'].tolist(),
['self', 'close', 'distal'])
self.assertListEqual(_prot_scores(s2_1), [0.9375, 0.875, 0.6875])
self.assertEqual(s2_1['match'], '620')
