如何在ID行后面加上值行的文件中按ID对行进行分组？

Question

我生成的序列文件如下：

>rpl-7
ATGGCTCCAAC
>rpl-7
AAGAAAGTGCCACAGGTTCCAGAAAC
>rpl-8
AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGC
>rpl-8
GCTCTCCAGATCCTCCGTCTTCGTCAGATCAA
>rpl-8
AAGTTCAACATCATCTGTCTTGAGGA

我想合并相同ID的序列，就像这样：

>rpl-7
ATGGCTCCAAC
AAGAAAGTGCCACAGGTTCCAGAAAC
>rpl-8
AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGC
GCTCTCCAGATCCTCCGTCTTCGTCAGATCAA
AAGTTCAACATCATCTGTCTTGAGGA

我使用python判断以‘>’开头的字符串是否相同，如果它们是相同的，则继续增加序列.但是，这种方法不能输出第一个ID.In添加，我认为使用 awk 会更容易，不幸的是我不熟悉awk。你知道怎么做吗？谢谢。

Answer 1

循环输入文件，分组到以rpl-id为键的字典，并将这些值附加到列表中：

rpl_dict = {}

with open('rpl_input.txt') as rpl_input_file:
    lines = rpl_input_file.readlines()
    for line in lines:
        # Fetching current `rpl-id`
        if line.startswith('>rpl'):
            rpl_key = line.strip()
        # Fetching current `rpl-value`
        else:
            rpl_value = line.strip()
            # Appending current `rpl-value`
            if rpl_key not in rpl_dict.keys():
                rpl_dict[rpl_key] = []
            rpl_dict[rpl_key].append(rpl_value)

# {'>rpl-7': ['ATGGCTCCAAC', 'AAGAAAGTGCCACAGGTTCCAGAAAC'], '>rpl-8': ['AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGC', 'GCTCTCCAGATCCTCCGTCTTCGTCAGATCAA', 'AAGTTCAACATCATCTGTCTTGAGGA']}
print(rpl_dict)

with open('rpl_output.txt', 'w') as rpl_output_file:
    for rpl_id, rpl_values in rpl_dict.items():
        rpl_output_file.write(f'{rpl_key}\n')
        for v in rpl_values:
            rpl_output_file.write(f'{v}\n')

输出文件：

>rpl-8
ATGGCTCCAAC
AAGAAAGTGCCACAGGTTCCAGAAAC
>rpl-8
AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGC
GCTCTCCAGATCCTCCGTCTTCGTCAGATCAA
AAGTTCAACATCATCTGTCTTGAGGA

Answer 2

你可以用regex来做这件事。由于您提到了文件，我添加了新的行字符，您可以用文件的内容替换它。

import re

regex = r'rpl-\d\n.*(?:$|\n)'
dic = {}
test_str = (">rpl-7\n"
    "ATGGCTCCAAC\n"
    ">rpl-7\n"
    "AAGAAAGTGCCACAGGTTCCAGAAAC\n"
    ">rpl-8\n"
    "AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGC\n"
    ">rpl-8\n"
    "GCTCTCCAGATCCTCCGTCTTCGTCAGATCAA\n"
    ">rpl-8\n"
    "AAGTTCAACATCATCTGTCTTGAGGA\n")

matches = re.finditer(regex, test_str, re.MULTILINE)

for  match in matches:
    rpl,pro = match.group().split('\n')
    if rpl in dic:
        dic[rpl] = dic[rpl]+pro
    else:
        dic[rpl] = pro

输出：

{'rpl-7': 'ATGGCTCCAACAAGAAAGTGCCACAGGTTCCAGAAAC',
 'rpl-8': 'AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGCGCTCTCCAGATCCTCCGTCTTCGTCAGATCAAAAGTTCAACATCATCTGTCTTGAGGA'}

Answer 3

这是另一个解决办法，

input_ = """>rpl-7
ATGGCTCCAAC
>rpl-7
AAGAAAGTGCCACAGGTTCCAGAAAC
>rpl-8
AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGC
>rpl-8
GCTCTCCAGATCCTCCGTCTTCGTCAGATCAA
>rpl-8
AAGTTCAACATCATCTGTCTTGAGGA"""

results = {}

lines = input_.splitlines()
for i, j in zip(lines[::2], lines[1::2]):
    results.setdefault(i, []).append(j)

for i, j in results.items():
    print(i)
    print("\n".join(j))

>rpl-7
ATGGCTCCAAC
AAGAAAGTGCCACAGGTTCCAGAAAC
>rpl-8
AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGC
GCTCTCCAGATCCTCCGTCTTCGTCAGATCAA
AAGTTCAACATCATCTGTCTTGAGGA