for key in temp_locus_description: if locus_description.has_key(key): locus_description[key] = chain(locus_description[key], temp_locus_description[key]) else: locus_description[key] = temp_locus_description[key] return locus_description def write_locus_description(locus_description): output_file = open("translation_analysis.txt", "w") for key in locus_description: for description in locus_description[key]: line = chain([key], description.strip().split("\t")) # pdb.set_trace() output_file.write('\t'.join(map(str, line))) output_file.write('\n') output_file.close() """ args[0]: Known gene network (LGN) args[1]: path to folder of output file """ if __name__ == '__main__': print "# loading not translated locus..." file_name = "not_translated_locus.csv" not_translated_locus = cf.read_node_unweighted(file_name) print "# locus - probe translationg analysis" translation_analysis(list(not_translated_locus), "affy_ATH1_array_elements-2010-12-20.txt")
epilog = """ This program gave general information for graph network """ # parse options: parser = MyParser(usage, description=description,epilog=epilog) parser.add_option("-d", "--delimiter", dest="delimiter", default="\t", help="delimiter of input & output files [default: tab]") (options, args) = parser.parse_args() if len(args) != 2: parser.error("incorrect number of arguments") delimiter = options.delimiter if delimiter == '\\t': delimiter = '\t' print "# loading network from edgelist..." basename = os.path.splitext(args[0])[0] LGN = cf.read_node_unweighted(args[0]) expansion_lists = read_result_from_one_iteration(args[1], delimiter=delimiter) probes_from_expansion = merge_nodes_from_expansion_lists(expansion_lists) G = frequency_computation(expansion_lists) write_frequency(G) subLGNs = create_list_subLGN(D, SIZE_OF_SUBLGN, LGN) internal_assessment(probes_from_expansion, LGN, subLGNs, G, D)