Question

我有以下功能（属于一个类）：

import Bio
from bioservices import KEGGParser, UniProt, QuickGO

def locate_common_GO(self,list_of_genes,GO_term):

    #initialize variables and classes
    q = QuickGO()
    a = Retrieve_Data()
    b=[]

    #get the uniprot IDS using hugo2uniprot. hugo2uniprot is a custom method of my Retrieve_Data class (which uses bioservices module) simply for getting a uniprot ID from a gene symbol. 
    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])


    #search for GO terms and store as dictionary. Keys are the gene name and a list of GO terms are values. 
    GO_dict = {}
    for i in range(0,len(b)):
        q = QuickGO()
        GO_dict[list_of_genes[i]]= q.Annotation(protein=b[i], frmt="tsv", _with=True,tax=9606, source="UniProt", col="goName")
    keys = GO_dict.keys()

    #This bit should search the dictionary values for a term supplied by the user (stored in the variable 'GO_Term'). 
    #If the user supplied term is present in the retrieved list of GO terms I want it to add the dictionary key (i.e. the gene name) to a list named 'matches'. 
    matches = []
    for gene in range(0,len(keys)):
        if GO_term in GO_dict[keys[gene]].splitlines():
            matches.append(keys[i])
    return matches

问题在于，尽管提供了具有已知共同基因术语的基因列表，但该功能的输出始终是相同的基因名称。例如，＆＃39; TGFB1＆＃39;和＆＃39; COL9A2＆＃39;两者都有一个GO术语蛋白质细胞外基质＆＃39;然而输出是一个列表，[＆＃39; COL9A2＆＃39;＆＃39; COL9A2＆＃39;]应该是[＆＃39; COL9A2＆＃39;＆＃39; TGFB1＆＃39;]。有没有人对如何修复这个程序有任何建议？我想我已经接近但我无法找到解决方案。

Answer 1

您始终将keys[i]附加到matches，但i在该循环中不会更改，因此您始终会附加相同的项目。您可能希望改为添加keys[gene]。

GO术语的生物信息检索以及与用户指定术语的比较

1 个答案: