def test_getBestFrontBackRecord(self):
"""Test function _parseBestFrontBackRecord()."""
obj = Classifier()
domFN = op.join(self.testDir, "data/test_parseHmmDom.dom")
front, back = obj._getBestFrontBackRecord(domFN)
# In the following, verify the front and back are equivalent
# to stdout/test_parseHmmDom_dFront/Back.txt
def prettystr(d):
"""Return Pretty print string for front & back."""
return "\n".join(
[key + ":\n" + "\n".join(
[k + ":" + str(v) for k, v in val.iteritems()])
for key, val in d.iteritems()])
frontFN = op.join(self.testDir, "out/test_parseHmmDom_dFront.txt")
backFN = op.join(self.testDir, "out/test_parseHmmDom_dBack.txt")
f = open(frontFN, 'w')
f.write(prettystr(front))
f.close()
f = open(backFN, 'w')
f.write(prettystr(back))
f.close()
stdoutFrontFN = op.join(self.testDir,
"stdout/test_parseHmmDom_dFront.txt")
stdoutBackFN = op.join(self.testDir,
"stdout/test_parseHmmDom_dBack.txt")
self.assertTrue(filecmp.cmp(frontFN, stdoutFrontFN))
self.assertTrue(filecmp.cmp(backFN, stdoutBackFN))
def test_pickBestPrimerCombo(self):
"""Test funciton _pickBestPrimerCombo()."""
obj = Classifier()
domFN = op.join(self.testDir, "data/test_parseHmmDom.dom")
front, back = obj._getBestFrontBackRecord(domFN)
# Now pick up the best primer combo
movie = "m131018_081703_42161_c100585152550000001823088404281404_s1_p0"
rids = [movie + "/" + str(zmw) + "/ccs" for zmw in [43, 45, 54]]
res = obj._pickBestPrimerCombo(
front[rids[0]], back[rids[0]], [0, 1], 10)
self.assertTrue(res[2] is None)
self.assertTrue(res[3] is None)
res = obj._pickBestPrimerCombo(
front[rids[1]], back[rids[1]], [0, 1], 10)
fw = DOMRecord("F1", movie + "/45/ccs", 33.0, 0, 30, 31, 0, 30, 100)
rc = DOMRecord("R1", movie + "/45/ccs", 27.2, 0, 25, 25, 0, 25, 100)
self.assertEqual(res[0], 1)
self.assertEqual(res[1], "+")
self.assertTrue(str(fw) == str(res[2]))
self.assertTrue(str(rc) == str(res[3]))
res = obj._pickBestPrimerCombo(
front[rids[2]], back[rids[2]], [0, 1], 10)
rc = DOMRecord("R1", movie + "/54/ccs", 22.3, 0, 25, 25, 0, 27, 100)
self.assertEqual(res[0], 1)
self.assertEqual(res[1], "+")
self.assertTrue(res[2] is None)
self.assertTrue(str(res[3]) == str(rc))
