Question

我正在尝试优化我的代码，因为当我尝试加载巨大的词典时，它变得非常慢。我认为这是因为它在词典中搜索一个键。我一直在阅读python defaultdict，我认为这可能是一个很好的改进，但我没有在这里实现它。正如您所看到的，是一个层次结构的字典结构。任何暗示都将受到赞赏。

class Species:
    '''This structure contains all the information needed for all genes.
    One specie have several genes, one gene several proteins'''
    def __init__(self, name):
        self.name = name #name of the GENE
        self.genes = {}
    def addProtein(self, gene, protname, len):
        #Converting a line from the input file into a protein and/or an exon
        if gene in self.genes:
            #Gene in the structure
            self.genes[gene].proteins[protname] = Protein(protname, len)
            self.genes[gene].updateProts()
        else:
            self.genes[gene] = Gene(gene) 
            self.updateNgenes()
            self.genes[gene].proteins[protname] = Protein(protname, len)
            self.genes[gene].updateProts()
    def updateNgenes(self):
    #Updating the number of genes
        self.ngenes = len(self.genes.keys())

基因和蛋白质的定义是：

class Protein:
    #The class protein contains information about the length of the protein and a list with it's exons (with it's own attributes)
    def __init__(self, name, len):
        self.name = name
        self.len = len

class Gene:
    #The class gene contains information about the gene and a dict with it's proteins (with it's own attributes)
    def __init__(self, name):
        self.name = name
        self.proteins = {}
        self.updateProts()
    def updateProts(self):
        #Update number of proteins
        self.nproteins = len(self.proteins)

Answer 1

您无法使用defaultdict，因为您的__init__方法需要参数。

这可能是你的瓶颈之一：

def updateNgenes(self):
#Updating the number of genes
    self.ngenes = len(self.genes.keys())

len(self.genes.keys())在计算长度之前创建所有键的list。这意味着每次添加基因时，都会创建一个列表并将其丢弃。你创建的这个列表越多，你拥有的基因就越多。要避免创建中间列表，只需执行len(self.genes)。

最好还是让ngenes成为property，这样才能在需要时进行计算。

@property
def ngenes(self):
    return len(self.genes)

nproteins类中的Gene也可以这样做。

以下是您重构的代码：

class Species:
    '''This structure contains all the information needed for all genes.
    One specie have several genes, one gene several proteins'''

    def __init__(self, name):
        self.name = name #name of the GENE
        self.genes = {}

    def addProtein(self, gene, protname, len):
        #Converting a line from the input file into a protein and/or an exon
        if gene not in self.genes:
            self.genes[gene] = Gene(gene) 
        self.genes[gene].proteins[protname] = Protein(protname, len)

    @property
    def ngenes(self):
        return len(self.genes)

class Protein:
    #The class protein contains information about the length of the protein and a list with it's exons (with it's own attributes)
    def __init__(self, name, len):
        self.name = name
        self.len = len

class Gene:
    #The class gene contains information about the gene and a dict with it's proteins (with it's own attributes)
    def __init__(self, name):
        self.name = name
        self.proteins = {}

    @property
    def nproteins(self):
        return len(self.proteins)

在分层字典中优化python密钥搜索

1 个答案: