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()
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()
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)
