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() result_filename = os.path.splitext(xml_filename)[0] + ".csv" result_filepath = helper.generate_filepath(pcimFolder, result_filename) we.write_expansion_list(result_filepath, expansion_list) result_PPV_filename = "%s%s" % \ (os.path.splitext(result_filename)[0], "_PPV.txt") result_SE_filename = "%s%s" % \ (os.path.splitext(result_filename)[0], "_SE.txt") result_PPV_filepath = helper.generate_filepath(pcimFolder, result_PPV_filename) result_SE_filepath = helper.generate_filepath(pcimFolder, result_SE_filename) we.write_statistical_result(result_PPV_filepath, IV.PPV) we.write_statistical_result(result_SE_filepath, IV.SE) # 2nd internal validation # IV2 = InternalValidationRls(genes_in_tiles, blocks, genes_in_lgn, edges_in_lgn) # expansion_list_2 = IV2.expansion_list() # expansion_filepath = helper.generate_filepath(pcimFolder, code)
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) expansion_list = IV.expansion_list() expansion_filepath = helper.generate_filepath(PCIM_FOLDER_1, xml_filename) we.write_expansion_list(expansion_filepath, expansion_list) # 2nd internal validation # IV2 = InternalValidationRls(genes_in_tiles, blocks, genes_in_lgn, edges_in_lgn) # expansion_list_2 = IV2.expansion_list() # expansion_filepath = helper.generate_filepath(PCIM_FOLDER_2, xml_filename) # we.write_expansion_list(expansion_filepath, expansion_list_2)