def run(self):
"""
03-01-05
initial
--db_connect()
--get_go_no2term_id() #for get_distance(), needs self.go_no2term_id
--data_fetch()
--gene_no2p_gene_setup()
--p_gene_id_map()
--_p_gene_map() or --_p_gene_map_network_topology()
--get_distance() #touches self.go_no2distance
--submit()
"""
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
curs.execute("begin") # because of cursor usage
self.go_no2term_id = get_go_no2term_id(curs, self.schema, self.term_table)
self.data_fetch(curs, self.p_gene_table, self.gene_p_table)
if self.type == 2 and self.pattern_table == None:
sys.stderr.write("\n type=2 needs pattern_table.\n")
sys.exit(3)
self.p_gene_map(
self.gene_no2p_gene,
self.p_gene_id_map,
curs,
self.distance_table,
self.go_no2distance,
self.go_no2term_id,
self.type,
)
if self.needcommit:
self.submit(curs, self.gene_p_table, self.p_gene_id_map)
curs.execute("end")
def dstruc_loadin(self, curs):
"""
03-14-05
remove the distance loading part
"""
sys.stderr.write("Loading Data STructure...\n")
from codense.common import get_known_genes_dict, get_go_no2go_id,\
get_go_no2term_id, get_go_no2depth, get_go_term_id2go_no, \
get_go_term_id2depth
self.known_genes_dict = get_known_genes_dict(curs)
self.go_no2go_id = get_go_no2go_id(curs)
self.go_no2term_id = get_go_no2term_id(curs)
self.go_no2depth = get_go_no2depth(curs)
self.go_term_id2go_no = get_go_term_id2go_no(curs)
self.go_term_id2depth = get_go_term_id2depth(curs)
sys.stderr.write("Done\n")
def return_go_no_map(self, go_no_list, curs, distance_table):
"""
03-06-05
input: a list of go_nos, curs
output: a map showing which go_no corresponds to which
curs is used to get the go_no2term_id and nodes pairwise distance
"""
sys.stderr.write("Mapping go_nos...")
from gene_p_map_redundancy import gene_p_map_redundancy
from codense.common import get_go_no2term_id
borrowed_instance = gene_p_map_redundancy()
go_no_map = {}
go_no2term_id = get_go_no2term_id(curs)
go_no2distance = {}
for i in range(len(go_no_list)):
go_no = go_no_list[i]
if go_no not in go_no_map:
#not flagged, map
go_no_map[go_no] = go_no
for j in range(i+1, len(go_no_list)):
go_no2 = go_no_list[j]
if go_no < go_no2:
key= (go_no, go_no2)
else:
key = (go_no2, go_no)
if key in go_no2distance:
jasmine_distance = go_no2distance[key][2]
else:
jasmine_distance = borrowed_instance.get_distance(curs, go_no, go_no2, distance_table, go_no2distance, go_no2term_id)
if jasmine_distance == 0:
#jasmine_distance=0 means they are parent-child
go_no_map[go_no2] = go_no
sys.stderr.write("done.\n")
return go_no_map