def run(self, data): logging.debug('Worker ID: ' + str(self.id) + ' Building finder ' '=========') logging.debug(data) kernel_file_url = data['kernel_url'] network_file_url = data['network_url'] query = data['query'] # Check finder exists or not if kernel_file_url in self.__finders.keys(): logging.debug('Kernel found. No need to create finder') finder = self.__finders[kernel_file_url] else: logging.debug('Building Finder...') generator = KernelGenerator() kernel = generator.create_kernel_from_file(kernel_file_url) network = util.read_sif(network_file_url) finder = SubNetworkFinder(kernel=kernel, network=network) self.__finders[kernel_file_url] = finder logging.debug('Building Finder... Done!') # Now find subnet logging.debug('******** Query: ' + str(query)) subnetwork = finder.get_sub_network(query) logging.debug('========== Sub Network found: Size = ' + str(len(subnetwork))) return subnetwork
def test_find_sub_network2(self): print('\n---------- Sub Network Finder tests 2 start -----------\n') from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder import hdsubnetfinder.subnetwork.network_util as util from hdsubnetfinder.kernel.kernel_generator import KernelGenerator generator = KernelGenerator() small_kernel = generator.create_kernel(network_url=NETWORK_URL) small_sif = util.read_sif(file_url=NETWORK_URL) finder = SubNetworkFinder(network=small_sif, kernel=small_kernel) identifiers = ["NRAS", "KRAS", "MAPK1"] result = finder.get_sub_network(identifiers) self.assertIsNotNone(result) print(len(result)) self.assertEqual(list, type(result)) print('\n---------- finder tests2 finished! -----------\n')
def test_find_sub_network(self): print('\n---------- Sub Network Finder tests start -----------\n') from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder import hdsubnetfinder.subnetwork.network_util as util # Create kernel from pre-computed kernel file generator = KernelGenerator() small_kernel = generator.create_kernel_from_file( pre_computed_kernel_url=SAMPLE_KERNEL_URL) small_sif = util.read_sif(file_url=NETWORK_URL) finder = SubNetworkFinder(network=small_sif, kernel=small_kernel) identifiers = ["NRAS", "KRAS", "MAPK1"] result = finder.get_sub_network(identifiers) self.assertIsNotNone(result) print(len(result)) self.assertEqual(list, type(result)) print('\n---------- finder tests finished! -----------\n')