Question

我有一个fasta文件（由> header和sequence行组成），如下所示：

myfasta

>S.sclerotiorum_Ch16_153_209
AACCCTAACCCTAACCCTTGATTGATTGATTGATTGATTGAT
TGATTGATGAAATTATAGTCTCCGTAAAGCAAATAAAGCATT
TAGTAAACGTTGAAGAGCTAGAAAAGCTTTAATACAAAAAGG
>S.sclerotiorum_Ch16_153_209
AACCCTAACCCTAACCCTTGATTGATTGATTGATTGATTGAT
TAGTAAACGTTGAAGAGCTAGAAAAGCTTTAATACAAAAAGG
>S.sclerotiorum_Ch14_442_1137
TGTCAATTCGATCTAGTATT
>S.sclerotiorum_Ch12_1831_180
AGAGCTAGAAAAGCTTTAAT
>S.sclerotiorum_Ch1_1831_180
AGAGCTAGAAAAGCTTTAATAGAGCTAGAAAAGCTTTAAT
AGAGCTAGAAAAGCTTTAATAGAGCTAGAAAAGCTTTAAT

我想按定义的顺序打印此文件（从Ch1到Ch16开始），并得到如下结果：

>S.sclerotiorum_Ch1_1831_180
AGAGCTAGAAAAGCTTTAATAGAGCTAGAAAAGCTTTAAT
AGAGCTAGAAAAGCTTTAATAGAGCTAGAAAAGCTTTAAT
>S.sclerotiorum_Ch12_1831_180
AGAGCTAGAAAAGCTTTAAT
>S.sclerotiorum_Ch14_442_1137
TGTCAATTCGATCTAGTATT
>S.sclerotiorum_Ch16_153_209
AACCCTAACCCTAACCCTTGATTGATTGATTGATTGATTGAT
TAGTAAACGTTGAAGAGCTAGAAAAGCTTTAATACAAAAAGG
>S.sclerotiorum_Ch16_153_209
AACCCTAACCCTAACCCTTGATTGATTGATTGATTGATTGAT
TGATTGATGAAATTATAGTCTCCGTAAAGCAAATAAAGCATT
TAGTAAACGTTGAAGAGCTAGAAAAGCTTTAATACAAAAAGG

我试图编写此代码，但是我的result.fasta中的输入文件的顺序仍然与我相同。任何帮助将不胜感激修复我的代码。谢谢！

代码：python code.py myfasta.fasta >> result.fasta

#!/usr/bin/env python
import sys
import os
import pathlib

myfasta = sys.argv[1]
fasta = open(myfasta)

#types = ['S.sclerotiorum_Ch16_', 'S.sclerotiorum_Ch15_', 'S.sclerotiorum_Ch14_', 'S.sclerotiorum_Ch13_', 'S.sclerotiorum_Ch12_', 'S.sclerotiorum_Ch11_', 'S.sclerotiorum_Ch10_', 'S.sclerotiorum_Ch9_', 'S.sclerotiorum_Ch8_', 'S.sclerotiorum_Ch7_', 'S.sclerotiorum_Ch6_', 'S.sclerotiorum_Ch5_', 'S.sclerotiorum_Ch4_', 'S.sclerotiorum_Ch3_', 'S.sclerotiorum_Ch2_', 'S.sclerotiorum_Ch1_']

types = ['S.sclerotiorum_Ch1', 'S.sclerotiorum_Ch2', 'S.sclerotiorum_Ch3', 'S.sclerotiorum_Ch4', 'S.sclerotiorum_Ch5', 'S.sclerotiorum_Ch6', 'S.sclerotiorum_Ch7', 'S.sclerotiorum_Ch8', 'S.sclerotiorum_Ch9', 'S.sclerotiorum_Ch10', 'S.sclerotiorum_Ch11', 'S.sclerotiorum_Ch12', 'S.sclerotiorum_Ch13', 'S.sclerotiorum_Ch14', 'S.sclerotiorum_Ch15', 'S.sclerotiorum_Ch16']




for type in range(len(types)):
    flag = False
    fasta = open(myfasta)
    for line in fasta:
        if line.startswith('>') and types[type] in line:
            flag = True
        elif line.startswith('>'):
          flag = False
        if flag:
            #grabbed = line.strip()
            #newfasta.writelines(grabbed + "\n")
            print(line.strip())

fasta.close

Answer 1

您可以将re.findall用于与某行匹配的模式，然后再匹配以非{>字符开头的行，并在Ch之后将数字分组，请使用{{1} }根据数字对匹配项进行排序，然后使用sorted将排序后的子字符串重新连接回字符串：

str.join

给出您存储在import re ''.join(s for s, _ in sorted(re.findall(r'(.*_Ch(\d+)_.*\n(?:[^>].*\n)*)', f), key=lambda t: int(t[1])))中的输入字符串（您应该先将整个文件读入此变量），这将返回：

使用python

1 个答案: