本文整理汇总了Python中Network.gene_list方法的典型用法代码示例。如果您正苦于以下问题：Python Network.gene_list方法的具体用法？Python Network.gene_list怎么用？Python Network.gene_list使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Network的用法示例。
在下文中一共展示了Network.gene_list方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: read_output
# 需要导入模块: import Network [as 别名]
# 或者: from Network import gene_list [as 别名]
def read_output(self,settings):
# Code to write for collecting the output files from the algorithm, writes to the
# output list in the object
# What we want to do here is get the prediction rate on the last time
# point and the network so we can compare it against a gold std.
# This file is a bunch of zscores, so we have to load the cutoff we want
output_file = open(self.output_dir + "/output/ranked_edges.txt", 'r')
topn = None
if "top_n_edges" in settings["genie3"].keys():
topn = settings["genie3"]["top_n_edges"]
else:
topn = len(self.gene_list)
zscores = []
for line in output_file:
gene1, gene2, zscore = line.split()
zscore = float(zscore)
zscores.append((gene1, gene2, zscore))
zscores = sorted(zscores, key=lambda zscore: abs(zscore[2]), reverse=True)
self.zscores = zscores[:]
network = []
#for i,zscore in enumerate(zscores):
#if i < topn:
#gene1, gene2, zscore = zscore
#zscores[i] = (gene1, gene2, 1)
#else:
#gene1, gene2, zscore = zscore
#zscores[i] = (gene1, gene2, 0)
net = Network()
net.read_networklist(zscores)
net.gene_list = self.gene_list
self.network = net
return self.zscores示例2: read_output
# 需要导入模块: import Network [as 别名]
# 或者: from Network import gene_list [as 别名]
def read_output(self,settings):
# Code to write for collecting the output files from the algorithm, writes to the
# output list in the object
# What we want to do here is get the prediction rate on the last time
# point and the network so we can compare it against a gold std.
# This file is a bunch of zscores, so we have to load the cutoff we want
output_file = open(self.output_dir + "/output/mcz_output.txt", 'r')
output_file = output_file.readlines()
zscores = []
for g1, line in enumerate(output_file[1:]):
for g2, val in enumerate(line.split('\t')[1:]):
zscores.append((self.gene_list[g2], self.gene_list[g1], float(line.split()[1:][g2])))
topn = settings["mcz"]["top_n_edges"]
#for line in output_file:
#gene1, gene2, zscore = line.split()
#zscore = float(zscore)
#zscores.append((gene1, gene2, zscore))
zscores = sorted(zscores, key=lambda zscore: abs(zscore[2]), reverse=True)
self.zscores = zscores[:]
network = []
#for i,zscore in enumerate(zscores):
#if i < topn:
#gene1, gene2, zscore = zscore
#if zscore > 0:
#zscores[i] = (gene1, gene2, 1)
#if zscore < 0:
#zscores[i] = (gene1, gene2, -1)
#else:
#gene1, gene2, zscore = zscore
#zscores[i] = (gene1, gene2, 0)
net = Network()
net.read_networklist(zscores)
net.gene_list = self.gene_list
self.network = net
return self.network示例3: JobManager
# 需要导入模块: import Network [as 别名]
# 或者: from Network import gene_list [as 别名]
cnlo_storage.normalize()
cnlo_no3_storage.normalize()
#all_storage.normalize()
ts_storage = [kno3_1, kno3_2, kno3_3, kno3_4]
#for s in ts_storage:
#s.normalize()
# Setup job manager
jobman = JobManager(settings)
# Figure out list of dex targets and put them into a network so we can
# compare
net = Network()
net.gene_list = dex_storage.gene_list
target = sys.argv[1]
if target == "At1g25550":
dex_storage = dex_storage2
for gene1 in dex_storage.gene_list:
net.network[gene1] = {}
for gene2 in dex_storage.gene_list:
net.network[gene1][gene2] = 0
for gene in dex_storage.gene_list:
print dex_storage.experiments[0].ratios[gene]
if dex_storage.experiments[0].ratios[gene] >= 2.0:
print dex_storage.experiments[0].ratios[gene]
net.network[target][gene] = 1
elif dex_storage.experiments[0].ratios[gene] <= 0.5: