def fill_edge2encodedOccurrence(self, sig_vector_fname, min_sup, max_sup, total_vertex_set=None):
"""
04-04-06
"""
sys.stderr.write("Getting edge2encodedOccurrence...\n")
from MpiFromDatasetSignatureToPattern import encodeOccurrenceBv
edge2encodedOccurrence = {}
reader = csv.reader(open(sig_vector_fname), delimiter='\t')
no_of_datasets = 0
counter = 0
for row in reader:
edge = row[:2]
edge = map(int, edge)
#04-06-06 any vertex of the edge doesn't appear in total_vertex_set, skip the edge
if total_vertex_set and (edge[0] not in total_vertex_set or edge[1] not in total_vertex_set):
continue
edge.sort() #04-06-06 in ascending order
sig_vector = row[2:]
sig_vector = map(int, sig_vector)
if no_of_datasets==0:
no_of_datasets = len(sig_vector)
if sum(sig_vector)>=min_sup and sum(sig_vector)<=max_sup:
edge2encodedOccurrence[tuple(edge)] = encodeOccurrenceBv(sig_vector)
sys.stderr.write("Done.\n")
del reader
return edge2encodedOccurrence, no_of_datasets
def fill_edge2encodedOccurrence(
self, hostname, dbname, schema, edge2encodedOccurrence, min_sup, max_sup, edge_table="edge_cor_vector"
):
"""
09-05-05
get the edge2encodedOccurrence from the database
"""
sys.stderr.write("Getting edges...\n")
(conn, curs) = db_connect(hostname, dbname, schema)
curs.execute(
"DECLARE crs CURSOR FOR select edge_name,sig_vector \
from %s"
% (edge_table)
)
curs.execute("fetch 5000 from crs")
rows = curs.fetchall()
no_of_datasets = 0
counter = 0
while rows:
for row in rows:
edge = row[0][1:-1].split(",")
edge = map(int, edge)
sig_vector = row[1][1:-1].split(",")
sig_vector = map(int, sig_vector)
if no_of_datasets == 0:
no_of_datasets = len(sig_vector)
if sum(sig_vector) >= min_sup and sum(sig_vector) <= max_sup:
edge2encodedOccurrence[tuple(edge)] = encodeOccurrenceBv(sig_vector)
curs.execute("fetch 5000 from crs")
rows = curs.fetchall()
sys.stderr.write("Done.\n")
return no_of_datasets
def get_recurrence_go_no_rec_array_cluster_id_ls(self, curs, pattern_table, mcl_id2go_no_set):
"""
2006-09-26
from pattern_table and use mcl_id2go_no_set
go_no_list is the go_id Set
mcl_id2enc_recurrence is for get_recurrence_rec_array_bs_no_list()
"""
sys.stderr.write("Getting recurrence_go_no_rec_array_cluster_id_ls...\n")
no_of_datasets = 0
go_no2recurrence_cluster_id = {}
mcl_id2enc_recurrence = {}
curs.execute("DECLARE crs CURSOR FOR SELECT id, recurrence_array from %s"\
%pattern_table)
curs.execute("fetch 5000 from crs")
rows = curs.fetchall()
counter = 0
real_counter = 0
while rows:
for row in rows:
mcl_id, recurrence_array = row
if mcl_id in mcl_id2go_no_set:
#if this pattern has functions predicted
recurrence_array = recurrence_array[1:-1].split(',')
recurrence_array = map(float, recurrence_array) #this is not a binary 0/1 array
occurrence_cutoff_func = lambda x: int(x>=0.8) #0.8 is arbitrary
recurrence_array = map(occurrence_cutoff_func, recurrence_array)
if no_of_datasets == 0:
no_of_datasets = len(recurrence_array)
go_no_list = mcl_id2go_no_set[mcl_id]
encoded_recurrence = encodeOccurrenceBv(recurrence_array)
mcl_id2enc_recurrence[mcl_id] = encoded_recurrence #2006-09-26
for go_no in go_no_list:
if go_no not in go_no2recurrence_cluster_id:
go_no2recurrence_cluster_id[go_no] = [encoded_recurrence, Set([mcl_id])]
#use Set() because mcl_id has duplicates due to different p-values
else:
go_no2recurrence_cluster_id[go_no][0] = \
go_no2recurrence_cluster_id[go_no][0] | encoded_recurrence
go_no2recurrence_cluster_id[go_no][1].add(mcl_id)
real_counter += 1
counter += 1
if self.report:
sys.stderr.write("%s%s\t%s"%('\x08'*20, counter, real_counter))
curs.execute("fetch 5000 from crs")
rows = curs.fetchall()
curs.execute("close crs")
recurrence_go_no_rec_array_cluster_id_ls = []
for go_no in go_no2recurrence_cluster_id:
encoded_recurrence, mcl_id_set = go_no2recurrence_cluster_id[go_no]
recurrence_array = decodeOccurrence(encoded_recurrence) #not binary vector
recurrence = len(recurrence_array)
recurrence_go_no_rec_array_cluster_id_ls.append([recurrence, go_no, recurrence_array, mcl_id_set])
recurrence_go_no_rec_array_cluster_id_ls.sort()
sys.stderr.write("End getting recurrence_go_no_rec_array_cluster_id_ls.\n")
return recurrence_go_no_rec_array_cluster_id_ls, no_of_datasets, mcl_id2enc_recurrence
def get_gene2enc_array(self, gim_inputfname, gene_id2no):
sys.stderr.write("Getting gene2enc_array...\n")
reader = csv.reader(open(gim_inputfname), delimiter='\t')
gene2enc_array = {}
for row in reader:
no_of_occurrences, occ_array, gene_id = row[0], row[1:-1], row[-1]
if gene_id in gene_id2no:
gene_no = gene_id2no[gene_id]
occ_array = map(int, occ_array)
gene2enc_array[gene_no] = encodeOccurrenceBv(occ_array)
sys.stderr.write("End getting gene2enc_array.\n")
return gene2enc_array