计算特定ID的gc含量

Question

我有一本叫self.__sequences的字典，上面写着"ID:DNA序列“，下面是该字典的一部分

{
 '1111758': ('TTAGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCAGGCCTAA\n', ''), 
 '1111762': ('AGAGTTTGATCCTGGCTCAGATTGA\n', ''),
 '1111763': ('AGAGTTTGATCCTGGCCTT\n', '')
}

我想要计算特定序列ID (some_id)的gc conent。也就是说，如果some_id在字典中，返回该ID的DNA序列的gc内容；如果some_id不存在，则返回一条错误消息。

Ps.gc content= (G+C)/(A+T+G+C)

我编写了以下代码(函数在类下)，但它提供了错误消息。如果有人能帮我改进我的代码，我很感激。

def compute_gc_content(self, some_id=''):
    """compute the gc conent for sequence ID (some_id). If some_id is in the  
dictionary, return the gc content of the DNA sequence for that ID; if some_id 
does not exist,return an error message"""

self.some_id = some_id
    for i in range(len(self.__sequences)):
    if self.some_id in self.__sequences.keys():
        return (self.some_id.values['G']+self.some_id.values['C'])/float(len(self.__sequences))
    else:
        return "This ID does not exist"

因此，如果我打印compute_gc_content('1111758')，我想打印gc内容的值，比如0.23。

Answer 1

我不确定我是否正确理解你。

def compute_gc_content(self, some_id=''):

    if some_id in self.__sequences:
        seq = self.__sequences['some_id'][0]
        return (seq.count('G')+seq.count('C'))/float(len(seq))
    else:
        return "This ID does not exist"

不需要使用in self.__sequences.keys()，in self.__sequences也做同样的事情。

Answer 2

这就是你要找的吗？

import itertools

class gc:
    def __init__(self):
        self.__sequences = {'1111758': ('TTAGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCAGGCCTAA\n', ''), '1111762': ('AGAGTTTGATCCTGGCTCAGATTGA\n', ''), '1111763': ('AGAGTTTGATCCTGGCCTT\n', '')}


def compute_gc_content(self, some_id=''):
    """compute the gc conent for sequence ID (some_id). If some_id is in the  
    dictionary, return the gc content of the DNA sequence for that ID; if some_id 
    does not exist,return an error message"""

    self.some_id = some_id
    for i in range(len(self.__sequences)):
        if self.some_id in self.__sequences.keys():
            return (float)(self.__sequences[some_id][0].count('G')+self.__sequences[some_id][0].count('C'))/(len(self.__sequences[some_id][0]))
        else:
            return "This ID does not exist"

print gc().compute_gc_content('1111758')