def test_write_dictionary_one_to_set_empty_path_works(self):
file_name = TestCase.id(self) + '_friends.txt'
self.assertFalse(os.path.exists(file_name),
msg='The file should not exist as precondition')
write_dictionary_one_to_set(self.friends, '', file_name)
self.assertTrue(os.path.exists(file_name),
msg='The file was not created')
os.remove(file_name)
def test_write_dictionary_one_to_set_non_existent_path_creates_file(self):
file_name = TestCase.id(self) + '_friends.txt'
file_path = 'a/path/'
self.assertFalse(os.path.exists(file_path + file_name),
msg='The file should not exist as precondition')
write_dictionary_one_to_set(self.friends, file_path, file_name)
self.assertTrue(os.path.exists(file_path + file_name),
msg='The file was not created')
os.remove(file_path + file_name)
os.rmdir('a/path/')
os.rmdir('a/')
def get_ppis(examples=10,
path_swissprot=config.PATH_SWISSPROT,
file_swissprot_proteins=config.FILE_SWISSPROT_PROTEINS,
url_swissprot=config.URL_SWISSPROT_PROTEINS,
path_reactome=config.PATH_REACTOME,
file_reactome_internal_edges=config.REACTOME_INTERACTIONS,
file_reactome_ppis=config.REACTOME_PPIS,
path_pathwaymatcher=config.PATH_TOOLS,
file_pathwaymatcher=config.FILE_PATHWAYMATCHER,
url_pathwaymatcher=config.URL_PATHWAYMATCHER):
"""Returns dictionary of lexicographical interactions: accessions --> accessions set"""
ppis = {}
if not os.path.exists(path_reactome + file_reactome_ppis):
create_pathwaymatcher_files(path_swissprot, file_swissprot_proteins,
url_swissprot, path_reactome,
file_reactome_internal_edges,
path_pathwaymatcher, file_pathwaymatcher,
url_pathwaymatcher)
print("Reading Reactome interactions...")
ppis = dictionaries.read_dictionary_one_to_set(
path_reactome,
file_reactome_internal_edges,
order_pairs=True,
col_indices=(0, 1),
ignore_header=True)
dictionaries.write_dictionary_one_to_set(ppis, path_reactome,
file_reactome_ppis)
else:
print("Reading Reactome unique interactions...")
ppis = dictionaries.read_dictionary_one_to_set(path_reactome,
file_reactome_ppis)
ppi_subset = {}
example = 0
if examples > 8000:
for key, values in ppis.items():
for value in values:
ppi_subset.setdefault(key.strip(), set()).add(value.strip())
example += 1
if example >= examples:
break
if example >= examples:
break
else:
random.seed(77)
keys = random.sample(list(ppis.keys()), int(examples))
for key in keys:
ppi_subset.setdefault(key.strip(), set()).add(
random.sample(ppis[key], 1)[0].strip())
print("Reactome interactions READY")
return ppi_subset
def test_write_dictionary_one_to_set_all_keys(self):
file_name = TestCase.id(self) + '_friends.txt'
self.assertFalse(os.path.exists(file_name),
msg='The file should not exist as precondition')
write_dictionary_one_to_set(self.friends, '', file_name)
with open(file_name) as file:
lines = file.readlines()
self.assertIn('David\tEster\n', lines, msg='Missing entry line')
self.assertIn('Michael\tDavid\n', lines, msg='Missing entry line')
self.assertIn('James\tMartha\n', lines, msg='Missing entry line')
os.remove(file_name)
def test_write_dictionary_one_to_set_one_row_each_set_entry(self):
"""Having a key with multiple values, writes one row for each key -- value pair"""
file_name = TestCase.id(self) + '_friends.txt'
self.assertFalse(os.path.exists(file_name),
msg='The file should not exist as precondition')
write_dictionary_one_to_set(self.friends, '', file_name)
with open(file_name) as file:
lines = file.readlines()
self.assertEqual(6,
len(lines),
msg='Wrong number of lines in the file')
self.assertIn('David\tEster\n', lines, msg='Missing entry line')
self.assertIn('David\tMartha\n', lines, msg='Missing entry line')
self.assertIn('David\tMathew\n', lines, msg='Missing entry line')
os.remove(file_name)
def test_write_dictionary_one_to_set_empty_file_name_raises_error(self):
with self.assertRaises(ValueError,
msg="Should not accept empty file name"):
write_dictionary_one_to_set({}, '', '')