def test_divided_to_species__names(self):
p = ParserBlast("divided_to_species.xml")
p.generate_xml_tree()
p.group_to_classes()
p.divide_to_species()
keys = sorted(['H**o sapiens', "Nomascus leucogenys"])
self.assertListEqual(sorted(p.name_of_species), keys)
def test_divided_to_species_predicted_names(self):
p = ParserBlast("divided_to_species.xml")
p.generate_xml_tree()
p.group_to_classes()
p.divide_to_species_predicted()
keys = sorted(
['Pan troglodytes', "Pongo abelii", "Nomascus leucogenys"])
self.assertListEqual(sorted(p.name_of_species_predicted), keys)
def test_divided_to_species_predicted_count(self):
p = ParserBlast("divided_to_species.xml")
p.generate_xml_tree()
p.group_to_classes()
p.divide_to_species_predicted()
count = 0
for i in p.species_predicted.keys():
count += len(p.species_predicted[i])
self.assertEqual(count, 4)
def test_group_to_class_synthetic_one_bad(self):
p = ParserBlast("group_to_class_all.xml")
p.generate_xml_tree()
p.group_to_classes()
p.synthetic.append(MainAlignment("Bad example", "123"))
values = [re.search("Synthetic", i.title) for i in p.synthetic]
self.assertIn(None, values)
def test_group_to_class_all_fill(self):
p = ParserBlast("group_to_class_all.xml")
p.generate_xml_tree()
p.group_to_classes()
self.assertTrue(
len(p.rest) != 0 and len(p.synthetic) != 0
and len(p.predicted) != 0 and len(p.weird) != 0)
def test_generate_xml_tree_good(self):
p = ParserBlast("good_file.xml")
p.generate_xml_tree()
self.assertTrue(len(p.main_alignments) != 0)
def test_divided_to_species_predicted_number_uniq(self):
p = ParserBlast("divided_to_species.xml")
p.generate_xml_tree()
p.group_to_classes()
p.divide_to_species_predicted()
self.assertTrue(len(p.species_predicted) == 3)
def test_one_hsp(self):
p = ParserBlast("good_file.xml")
p.generate_xml_tree()
self.assertTrue(len(p.main_alignments[0].alignments) == 1)
def test_more_hsp(self):
p = ParserBlast("more_hsp.xml")
p.generate_xml_tree()
self.assertTrue(len(p.main_alignments[0].alignments) != 1)
def test_group_to_class_synthetic_all_good(self):
p = ParserBlast("group_to_class_all.xml")
p.generate_xml_tree()
p.group_to_classes()
values = [re.search("Synthetic", i.title) for i in p.synthetic]
self.assertNotIn(None, values)
def test_generate_xml_tree_bad(self):
p = ParserBlast("bad_file.xml")
p.generate_xml_tree()
self.assertRaises(IndexError)
self.assertTrue(len(p.main_alignments) == 0)