def jasmine_distance(self, go_id1, go_id2, lc_ancestors): min_distance = 100 for ancestor in lc_ancestors: distance1 = len(GraphAlgo.shortest_path(self.go_digraph, ancestor, go_id1))-1 distance2 = len(GraphAlgo.shortest_path(self.go_digraph, ancestor, go_id2))-1 if distance1 < min_distance: min_distance = distance1 if distance2 < min_distance: min_distance = distance2 return min_distance
def submit(self):
sys.stderr.write("Database transacting...")
#following string operations are because of format restrictions of database array input
string__unknown_gene_list = repr(self._unknown_gene_list)
string__unknown_gene_list = string__unknown_gene_list.replace("'", '')
string__unknown_gene_list = '{' + string__unknown_gene_list[1:-1] + '}'
string_unknown_gene_list = repr(self.unknown_gene_list)
string_unknown_gene_list = '{' + string_unknown_gene_list[1:-1] + '}'
self.curs.execute("insert into go(go_id, go_no, no_of_genes, name, whole_gene_array, gene_array, depth) \
values('%s', %d, %d, '%s', '%s', '%s', 2)"%('GO:0000004', 0, len(self._unknown_gene_list), \
'biological_process unknown', string__unknown_gene_list, string_unknown_gene_list))
go_dict = self.parser.parse(self.go_inf, self.vertex_dict)
for term in go_dict:
string_whole_gene_array = repr(go_dict[term].whole_gene_array)
string_gene_array = repr(go_dict[term].gene_array)
string_whole_gene_array = string_whole_gene_array.replace("'", '')
string_whole_gene_array = '{' + string_whole_gene_array[1:-1] + '}'
string_gene_array = '{' + string_gene_array[1:-1] + '}'
go_dict[term].name = go_dict[term].name.replace("'",'')
depth = len(GraphAlgo.shortest_path(self.go_graph, 'GO:0008150', term))
self.curs.execute("insert into go(go_id, go_no, no_of_genes, name, whole_gene_array, gene_array, depth) \
values('%s', %d, %d, '%s', '%s', '%s', %d)"%(term, go_dict[term].no, go_dict[term].no_of_genes,\
go_dict[term].name, string_whole_gene_array, string_gene_array, depth))
if self.needcommit:
self.conn.commit()
sys.stderr.write("done.\n")
def raw_distance(self, go_id1, go_id2): distance = len(GraphAlgo.shortest_path(self.go_graph, go_id1, go_id2))-1 return distance
def depth_of_one_node(self, go_id): return len(GraphAlgo.shortest_path(self.go_digraph, self.root, go_id))