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)
