def postproc(pcResultFolder, pcimFolder, lgnFilePath) : code = DEFAULT_OUTPUT_FILENAME genes_in_lgn, edges_in_lgn = pl.read_lgn(lgnFilePath) list_of_expanded_network_file = pen.merge_different_pc_run(code, pcResultFolder) genes_in_tiles, blocks = pen.read_expanded_network(list_of_expanded_network_file) # 1st internal validation IV = InternalValidation(genes_in_tiles, blocks, genes_in_lgn, edges_in_lgn) expansion_list = IV.expansion_list()
XML_MAPPING_FOLDER = '../xml_mapping' PC_RESULT_FOLDER = '../expanded_network' LGN_FOLDER = '../lgns' PCIM_FOLDER_1 = '../pcim_result_1' PCIM_FOLDER_2 = '../pcim_result_2' xml_list = px.xml_list(XML_MAPPING_FOLDER) for xml_filepath in xml_list: # common things used in both type of internal validation xml_filename = os.path.basename(xml_filepath) obs_filename, lgn_filename = px.read_single_xml(xml_filepath) lgn_filepath = helper.generate_filepath(LGN_FOLDER, lgn_filename) genes_in_lgn, edges_in_lgn = pl.read_lgn(lgn_filepath) list_of_expanded_network_file = pen.merge_different_pc_run(xml_filename, PC_RESULT_FOLDER) # no expanded network found for this xml file # maybe the result will be run at a later time if len(list_of_expanded_network_file) == 0: continue genes_in_tiles, blocks = pen.read_expanded_network(list_of_expanded_network_file) print "Internal Validation for %s" % xml_filename # 1st internal validation IV = InternalValidation(genes_in_tiles, blocks, genes_in_lgn, edges_in_lgn)