如何对单个字典中的值进行配对比较？

Question

我有一个带有DNA序列的Fasta文件，我想对每个DNA序列进行配对比较。

fasta文件包含这样的形式。

>dna1
TAGTACTGACCATGGCGTTTGTTG
>dna2
ACCTTGAGATACAAAACGATTGGACTG
>dna3
GCTTCACTGATGCAGTATTCAATTAACCAG
>dna4
CCACTGGAGCTTTCCAAAGGG
>dna5
TCTGTGGGTCCGGTTGTACAG

我的方法是先从DNA序列的快速文件中建立一个字典 然后对字典中的值进行一对一的比较 找出每对序列之间的%age identity!

我在做配对比较的时候遇到了问题!

我的代码如下。

from collections import OrderedDict
from typing import Dict

# Convert the fasta file to dictionary
DnaName_SYMBOL = '>'
def parse_DNAsequences(filename: str,
                    ordered: bool=False) -> Dict[str, str]:
    # filename: str is the DNA sequence name
    # ordered: bool, Gives us an option to order the resulting dictionary

    result = OrderedDict() if ordered else {}

    last_name = None
    with open(filename) as sequences:
        for line in sequences:
            if line.startswith(DnaName_SYMBOL):
                last_name = line[1:-1]
                result[last_name] = []
            else:
                result[last_name].append(line[:-1])

    for name in result:
        result[name] = ''.join(result[name])

    return result
DNAdict = parse_DNAsequences('output.fas')

这部分是我的问题所在，在字典中迭代值。

def PairwiseComparison():
    match = sum(s1 == s2 for s1, s2 in zip(a,b))
    if len(s1) > len(s2):
        lengthchosen = len(s1)
    percentidentity = 100*match/lengthchosen

print('{} vs {} {}%').format(percentidentity)

输出结果应该是这样的

dna1 vs dna2 90%
dna1 vs dna3 100%
dna2 vs dna3 90%

其他说明 如果我们比较2个DNA序列，其中一个的长度大于另一个，那么我们就用这个长度来计算。身份百分比 二者之间

Answer 1

我想，你成功地创建了DNA的字典，我已经在我的例子上硬编码了。itertools.combinations

from itertools import combinations

dna_dict = {
    'dna1': 'TAGTACTGACCATGGCGTTTGTTG',
    'dna2': 'ACCTTGAGATACAAAACGATTGGACTG',
    'dna3': 'GCTTCACTGATGCAGTATTCAATTAACCAG'
}

def PairwiseComparison(d1, d2):
    match = sum(s1 == s2 for s1, s2 in zip(d1,d2))
    if len(d1) > len(d2):
        lengthchosen = len(d1)
    else:
        lengthchosen = len(d2)
    percentidentity = 100*match/lengthchosen

    return percentidentity

# Creates all the possible combinations of the dictionary keys
dna_combinations = combinations(dna_dict, 2)

for dna1, dna2 in dna_combinations:
    percent_identity = PairwiseComparison(dna_dict[dna1], dna_dict[dna2])
    print(f'{dna1} vs {dna2} {percent_identity}%')  # The f-strings need python > 3.6, you can change the format if you have a lower version

如果你需要任何澄清和补充，请随时添加评论。