我有以下代码:
import Bio
from bioservices import KEGGParser, UniProt, QuickGO
#start a new method of my custom 'Retrieve_Data' class
def locate_common_GO(self,list_of_genes,GO_term):
#initialize variables and classes
q = QuickGO()
a = Retrieve_Data()
b=[]
使用(自定义方法)hugo2uniprot获取uniprot id
for i in range(0,len(list_of_genes)):
b.append(a.hugo2uniprot(list_of_genes[i],'hsa'))
print 'Gene: {} \t UniProtID: {}'.format(list_of_genes[i],b[i])
搜索GO术语(使用bioservices QuickGO)并存储为字典
GO_dict = {}
q = QuickGO()
我得到的一些基因名称的大列表没有返回任何点击。 这些将导致我要处理的AttributeError,然后转到列表中的下一项。当前代码返回错误:AttributeError:“int”对象没有属性“split”。这个错误起源于bioservices模块(所以当我调用q.Annotation…)
for i in range(len(b)):
try:
GO_dict[list_of_genes[i]] = q.Annotation(protein=b[i], frmt="tsv", _with=True,tax=9606, source="UniProt", col="goName")
except AttributeError:
continue
#The rest of this code is irrelevant to my problem but I've included it for completeness:
#Essentially it is designed to locate specific keywords in the results of the above code and return the gene name that they came from.
keys = GO_dict.keys()
matches = []
for gene in range(0,len(keys)):
if GO_term in GO_dict[keys[gene]].splitlines():
matches.append(keys[gene])
return matches
有没有人建议让异常处理工作起来,从而完成对指定列表的迭代,而不是停止脚本?你知道吗
好吧,我刚刚意识到问题是错误来自不同的代码。。。所以我基本上什么都不想处理。我现在已经修好了,多亏了所有的人。你知道吗
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