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Copy pathtest_dab.py
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81 lines (65 loc) · 2.86 KB
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import unittest
import numpy
from flib.core.dab import Dab
class TestDab(unittest.TestCase):
def setUp(self):
self.dab_file = 'files/test_data/test_dab.dab'
self.dab = Dab(self.dab_file)
self.dat_filename = 'files/test_data/test_dat.dat'
self.dat_file = open(self.dat_filename)
self.dat = self.dat_file.readlines()
self.qdab_file = 'files/test_data/test_qdab.qdab'
self.qdab = Dab(self.qdab_file)
self.qdab_dat_filename = 'files/test_data/test_qdab.dat'
self.qdab_dat_file = open(self.qdab_dat_filename)
self.qdab_dat = self.qdab_dat_file.readlines()
def tearDown(self):
self.dat_file.close()
self.qdab_dat_file.close()
return
def test_open_dab(self):
# Test the total number of loaded genes
self.assertEqual(len(self.dab.gene_list), 16)
# Test the total number of values (16 choose 2)
self.assertEqual(len(self.dab.dat), 120)
def test_get_value(self):
# Test the values from Dab class with values from dab exported as dat
for l in self.dat:
g1, g2, value = l.strip().split('\t')
val = float(value)
dat_val = self.dab.get_value_genestr(g1, g2)
assert numpy.isclose(val, dat_val, rtol=1e-05, atol=1e-08)
def test_get(self):
for i, g1 in enumerate(self.dab.gene_list):
vals = self.dab.get(g1)
for j, g2 in enumerate(self.dab.gene_list):
if g1 == g2:
# Self interaction should be 1
self.assertEqual(vals[j], 1)
else:
# Test the values from dab.get match dab.get_value
self.assertEqual(
vals[j], self.dab.get_value_genestr(g1, g2))
def test_open_qdab(self):
# Test the total number of loaded genes
self.assertEqual(len(self.qdab.gene_list), 16)
# Test the total number of values (16 choose 2)
self.assertEqual(len(self.qdab.dat), 120)
def test_qdab_get_value(self):
# Test the values from Dab class with values from dab exported as dat
for l in self.qdab_dat:
g1, g2, value = l.strip().split('\t')
val = float(value)
dat_val = self.qdab.get_value_genestr(g1, g2)
assert numpy.isclose(val, dat_val, rtol=1e-05, atol=1e-08)
def test_qdab_get(self):
for i, g1 in enumerate(self.qdab.gene_list):
vals = self.qdab.get(g1)
for j, g2 in enumerate(self.qdab.gene_list):
if g1 == g2:
# Self interaction should be 1
self.assertEqual(vals[j], 1)
else:
# Test the values from dab.get match dab.get_value
self.assertEqual(
vals[j], self.qdab.get_value_genestr(g1, g2))