Python get_testing_configurationの例

コード例 #1

import unittest
import datetime
import logging
import os

from pasta.test import get_testing_configuration, data_source_path, TestLevel, is_test_enabled
from pasta import get_logger
from pasta.tree import PhylogeneticTree
from pasta.alignment import SequenceDataset
from pasta.treeholder import read_and_encode_splits
from pasta.pastaalignerjob import bisect_tree

TOL = 0.000001
_LOG = get_logger(__name__)
config = get_testing_configuration()


class DecompTest(unittest.TestCase):
    def testLongestEdge(self):
        sd = SequenceDataset()
        fp = data_source_path('100T.fasta')
        sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')
        fp = data_source_path('100T.tree')
        tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU"))
        self.assertEqual(len(tree_list), 1)
        t = PhylogeneticTree(tree_list[0])
        self._do_test_longest(t)

    def testCentroidEdge(self):
        sd = SequenceDataset()

コード例 #2

ファイル: test_decomp.py プロジェクト: SagesWang/pasta

import unittest
import datetime
import logging
import os

from pasta.test import get_testing_configuration, data_source_path, TestLevel, is_test_enabled
from pasta import get_logger
from pasta.tree import PhylogeneticTree
from pasta.alignment import SequenceDataset
from pasta.treeholder import read_and_encode_splits
from pasta.pastaalignerjob import bisect_tree

TOL = 0.000001
_LOG = get_logger(__name__)
config = get_testing_configuration()

class DecompTest(unittest.TestCase):

    def testLongestEdge(self):
        sd = SequenceDataset()
        fp = data_source_path('100T.fasta')
        sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')
        fp = data_source_path('100T.tree')
        tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU"))
        self.assertEqual(len(tree_list), 1)
        t = PhylogeneticTree(tree_list[0])
        self._do_test_longest(t)

    def testCentroidEdge(self):
        sd = SequenceDataset()