def close_connected_nodes(self):
for node in self._nodesIn_:
if not node._stop_flag_.is_set():
node.close_connection('Server being shut down')
node.join()
for node in self._nodesOut_:
if not node._stop_flag_.is_set():
node.close_connection('Server being shut down')
node.join()
def process_orthologs(filename, nodes, gene_to_num):
with open(filename, 'r') as file:
for line in file.readlines():
blocks = line.split();
if blocks[0] != "Ensembl":
i = gene_to_num[blocks[0]]
for gene in blocks:
if gene in gene_to_num: #some orthologs could be from additional chromosomes
j = gene_to_num[gene]
node.join(nodes, i, j)
def process_paralogs(filename, nodes, gene_to_num):
with open(filename, 'r') as file:
for line in file.readlines():
blocks = line.split()
if blocks[0] != "Ensembl":
if len(blocks) == 1:
continue
if blocks[1] in gene_to_num: #some paralogs could be from additional chromosomes
i = gene_to_num[blocks[0]]
j = gene_to_num[blocks[1]]
node.join(nodes, i, j)
def pgma(seq_names, seqs, score_matrix, kind):
n = len(seqs)
nodes = [node.Node(i, seq_names[i], seqs[i]) for i in range(0, n)]
count = [1 for _ in range(0, n)]
scores = [[0 for _ in range(0, n)] for _ in range(0, n)]
minus_infinity = -10000000000
for i in range(0, n):
for j in range(i + 1, n):
score = pairwise_alignment.seq_alignment(seqs[i], seqs[j], score_matrix)
scores[i][j] = score
scores[j][i] = score
for i in range(0, n):
scores[i][i] = minus_infinity
clusters = {}
for i in range(0, n):
clusters[i] = 1
for _ in range(0, n - 1):
argmax1 = -1
argmax2 = -1
max = minus_infinity
for i in range(0, n):
if i in clusters:
for j in range(i + 1, n):
if j in clusters:
if scores[i][j] > max:
max = scores[i][j]
argmax1 = i
argmax2 = j
i1, i2 = node.join(nodes, argmax1, argmax2, score_matrix) # first will present new cluster
#recalc_scores
if kind == 'w':
for k in range(0, n):
if k != i1:
new_score = float(scores[i1][k] + scores[i2][k]) / 2
scores[i1][k] = new_score
scores[k][i1] = new_score
else:
for k in range(0, n):
if k != i1:
new_score = float(scores[i1][k] * count[i1] + scores[i2][k] * count[i2]) / (count[i1] + count[i2])
scores[i1][k] = new_score
scores[k][i1] = new_score
del clusters[i2]
count[i1] += count[i2]
root_index = node.find(nodes, 0)
return nodes[root_index].seq_names, nodes[root_index].seqs
def neigbor_joining(seq_names, seqs, score_matrix):
n = len(seqs)
nodes = [node.Node(i, seq_names[i], seqs[i]) for i in range(0, n)]
count = [1 for _ in range(0, n)]
scores = [[0 for _ in range(0, n)] for _ in range(0, n)]
minus_infinity = -10000000000
for i in range(0, n):
for j in range(i + 1, n):
score = pairwise_alignment.seq_alignment(seqs[i], seqs[j], score_matrix)
scores[i][j] = score
scores[j][i] = score
for i in range(0, n):
scores[i][i] = 0
clusters = {}
for i in range(0, n):
clusters[i] = 1
for lolo in range(0, n - 1):
argmax1 = -1
argmax2 = -1
max = minus_infinity
r = len(clusters)
for i in range(0, n):
if i in clusters:
for j in range(i + 1, n):
if j in clusters:
score = scores[i][j] * (r - 2) - sum_scores(scores[i], clusters) - sum_scores(scores[j], clusters)
if score > max:
max = score
argmax1 = i
argmax2 = j
i1, i2 = node.join(nodes, argmax1, argmax2, score_matrix) # first will present new cluster
#recalc_scores
for k in range(0, n):
if k != i1 and k!= i2:
new_score = float(scores[i1][k] + scores[i2][k] - scores[i1][i2]) / 2
scores[i1][k] = new_score
scores[k][i1] = new_score
del clusters[i2]
count[i1] += count[i2]
root_index = node.find(nodes, 0)
return nodes[root_index].seq_names, nodes[root_index].seqs
def join_ring(node_name, node_port):
othernode = node.Node_Info(node_name, node_port)
node.join(othernode)
node.thisNode = node.Node_Info(node.IPAddr, node.ctrlPort)
Internal_service = serve.Internal_Service()
node.add_service(Internal_service)
node.add_service(serve.ECHO_service())
node.net_server = start(node.thisNode, node.handle_message)
database = db.Shelver("test.db")
node.add_service(database)
TOPO = Topology_Service.Topology()
node.add_service(TOPO)
if len(sys.argv) > 2:
node_name = sys.argv[2]
node_port = int(sys.argv[3])
othernode = node.Node_Info(node_name, node_port)
node.join(othernode)
print node.thisNode
print othernode
#f = lambda : node.join(othernode)
#t = Thread(target=f)
#t.start()
else:
node.create()
#t = Thread(target = node.create)
#t.start()
node.startup()
while True:
cmd = raw_input(">>")
if cmd[:6] == "get f ":
x = int(cmd[6:])
print node.fingerTable[x]