如何在 ID 行后跟值行的文件中按 ID 对行进行分组？

Question

我生成的序列文件如下：>rpl-7ATGGCTCCAAC>rpl-7AAGAAAGTGCCACAGGTTCCAGAAAC>rpl-8AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGC>rpl-8GCTCTCCAGATCCTCCGTCTTCGTCAGATCAA>rpl-8AAGTTCAACATCATCTGTCTTGAGGA我想合并相同ID的序列，就像这样：>rpl-7ATGGCTCCAACAAGAAAGTGCCACAGGTTCCAGAAAC>rpl-8AAGAACAAGGAGAAGAAGACCCAATACTTCAAGCGTGCGCTCTCCAGATCCTCCGTCTTCGTCAGATCAAAAGTTCAACATCATCTGTCTTGAGGA我用python判断以'>'开头的字符串是否相同，如果相同则继续增加序列。但是，这种方法无法输出第一个ID。另外，我认为使用awk会更容易，不幸的是我对 awk 不熟悉。你知道该怎么做吗？谢谢。

Answer 1

循环输入文件，使用rpl-idas 键分组到字典并将值附加到列表中：

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

这是另一个解决方案，

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

Answer 3

您可以使用正则表达式来执行此操作。由于您提到文件，我添加了新行字符，您可以将其替换为文件的内容。

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'}