def kMax_parser(self, inf):
#initlialize the cluster_set data structure
cluster_set = []
#for dumb purpose
parameter = ''
#first line contains the splat_id
line = inf.readline()
splat_id = int(line[2:-1])
#second line contains the parameter, old kMax_batch_run.py doesn't output the parameter
line = inf.readline()
parameter = line[2:-1]
inf2 = cStringIO.StringIO(inf.read())
iter = splat_result_iterator(inf2)
for pattern in iter:
#initlialize the set first
vertex_set = Set()
#first line is no_of_edges
line = pattern.readline()
no_of_edges = int(line[:-1])
#second line is recurrence pattern, ignore.
line = pattern.readline()
#from the third line, it's the edge_set
line = pattern.readline()
while line !='\n':
edge_set = line[1:-2].split(')(')
for edge in edge_set:
vertex_list = edge.split()
vertex_set.add(int(vertex_list[0]))
vertex_set.add(int(vertex_list[1]))
line = pattern.readline()
#convert the set to list
vertex_list = list(vertex_set)
vertex_list.sort()
no_of_nodes = float(len(vertex_list))
connectivity = 2*no_of_edges/(no_of_nodes*(no_of_nodes-1))
unit = cluster(splat_id, vertex_list, parameter, connectivity)
cluster_set.append(unit)
return cluster_set
def parse_splat_results(self, splat_id, outfname, splat2db_instance, codense2db_instance, curs): """ 03-19-05 """ listOfMclResult = [] from splat_to_db import splat_result_iterator outf = open(outfname, 'r') iter = splat_result_iterator(outf) for pattern in iter: unit = MclResult() splat2db_instance.parse(pattern) edge_set = splat2db_instance.edge_set node_set = Set() for edge in edge_set: #in-situ sort, splat2db_instance.edge_set is also changed edge.sort() node_set.add(edge[0]) node_set.add(edge[1]) node_list = list(node_set) node_list.sort() no_of_nodes = len(node_list) no_of_edges = len(edge_set) #calculate the recurrence_array via codense2db_instance's functions combined_cor_vector, combined_sig_vector = codense2db_instance.get_combined_cor_vector(curs, edge_set) cor_cut_off = 0 #0 means no cut off for those edges. #all these are needed to submit to splat_result and mcl_result unit.splat_id = splat_id unit.vertex_set = node_list unit.edge_set = edge_set unit.connectivity = codense2db_instance.parse_connectivity(combined_sig_vector, no_of_edges, no_of_nodes) unit.recurrence_array = codense2db_instance.parse_recurrence(combined_sig_vector, \ len(edge_set), cor_cut_off) listOfMclResult.append(unit) outf.close() return listOfMclResult
