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import unittest
import os
from bp import parse_jplace, insert_fully_resolved
import skbio
import pandas as pd
class InsertTests(unittest.TestCase):
package = 'bp.tests'
def setUp(self):
with open(self.get_data_path('300/placement_mul.jplace'), 'r') as file:
self.jplacedata_multiple = file.read()
self.final_multiple_fully_resolved = \
skbio.TreeNode.read(self.get_data_path('300/placement.full_resolve.newick'))
def get_data_path(self, filename):
current_directory = os.getcwd()
return current_directory + "/tests/data/" + filename
def test_insert_fully_resolved(self):
exp = self.final_multiple_fully_resolved
placements, backbone = parse_jplace(self.jplacedata_multiple)
obs = insert_fully_resolved(placements, backbone)
self.assertEqual({n.name for n in obs.tips()},
{n.name for n in exp.tips()})
self.assertEqual(obs.compare_rfd(exp), 0)
self.assertAlmostEqual(obs.compare_tip_distances(exp), 0)
def test_insert_fully_resolved_multiple_placements(self):
exp = self.final_multiple_fully_resolved
placements, backbone = parse_jplace(self.jplacedata_multiple)
# add another placement elsewhere that we would not keep
# as it's ratio is lower
dup1 = placements.iloc[0].copy()
dup1['like_weight_ratio'] -= 0.5
dup1['edge_num'] += 1
# add another placement elsewhere that we would not keep
# as, though its ratio is the same, its pendant is larger
dup2 = placements.iloc[1].copy()
dup2['pendant_length'] += 0.5
dup2['edge_num'] += 1
placements = pd.concat([placements, pd.DataFrame([dup1, dup2])])
obs = insert_fully_resolved(placements, backbone)
self.assertEqual({n.name for n in obs.tips()},
{n.name for n in exp.tips()})
self.assertEqual(obs.compare_rfd(exp), 0)
self.assertAlmostEqual(obs.compare_tip_distances(exp), 0)
if __name__ == '__main__':
unittest.main()
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