Python 自动化提取基因的 CDS

一、环境准备及背景介绍

Python 开发环境：搭建 Python 高效开发环境： Pycharm + Anaconda

Biopython 序列处理：生物信息中的 Python 02 | 用biopython解析序列

示例 Genbank 数据：下载链接

Genbank 数据介绍：生物信息中的Python 05 | 从 Genbank 文件中提取 CDS 等其他特征序列

目录结构：

二、Python 实现

BaimoTools.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author  : Baimoc
# @Email   : baimoc@163.com
# @Time    : 2020/12/20 14:28
# @File    : BaimoTools
import os
import time

from Bio import SeqIO, SeqFeature


class BaimoTools():
    def __init__(self, gb_file, fasta_file):
        self.complete_fasta = ""
        self.fasta_file = fasta_file
        self.gb_file = gb_file
        self.feature = None
        self.record = None

    def format_val(self, object=None):
        """
        格式化对象值为字符串
        :param object: 对象或对象键值
        :return:
        """
        key = ""
        # 判断参数是否为字符
        if isinstance(object, str):
            obj = self.feature.qualifiers
            key = object
        else:
            obj = object
        # 为字符，提取 feature.qualifiers 对象关键字
        if key != "" and not obj.get(key):
            return ""
        elif key == "":
            val = obj
        else:
            val = obj[key]
        # 转换为字符串
        if not len(val):
            val = ""
        elif len(val) == 1:
            val = val[0]
        else:
            if isinstance(val, SeqFeature.CompoundLocation) or isinstance(val, SeqFeature.FeatureLocation):
                val = str(val)
            else:
                val = " | ".join(val)
        return val

    def extract_cds(self, cds):
        """
        获取 CDS 的 Fasta 序列
        :param cds: 获取指定基因的 CDS 区域，如果为空，则获取全部
        """
        records = list(SeqIO.parse(self.gb_file, "genbank"))
        for record in records:
            print(f"{record.id}")
            for feature in record.features:
                # 提取 CDS 信息
                if feature.type == "CDS":
                    self.feature = feature
                    self.record = record
                    cds_gene = self.format_val('gene')
                    if cds == "":
                        self.complete_fasta += self.format_fasta()
                    elif isinstance(cds, str) and cds_gene == cds:
                        self.complete_fasta += self.format_fasta()
                    elif isinstance(cds, list) and cds_gene in cds:
                        self.complete_fasta += self.format_fasta()
        self.write_file()

    def write_file(self):
        """
        写入文件
        """
        with open(self.fasta_file, "w") as f_obj:
            f_obj.writelines(self.complete_fasta)

    def format_fasta(self, num=0):
        """
        整理 Fasta 格式
        :param num: 每行字符数，超出则换行
        :return: Fasta 文本
        """
        cds_gene = self.format_val('gene')
        cds_location = self.format_val(self.feature.location)
        cds_product = self.format_val('product')
        cds_protein_id = self.format_val('protein_id')
        cds_translation = self.format_val('translation')
        complete_ana = f">{self.record.id} | {cds_gene} | {cds_product} | {cds_protein_id} | {str(cds_location)}\n"
        format_seq = ""
        if num:
            for i, char in enumerate(cds_translation):
                format_seq += char
                if (i + 1) % num == 0:
                    format_seq += "\n"
        else:
            format_seq = cds_translation
        return complete_ana + format_seq + "\n"

三、使用示例

数据介绍

示例数据为新冠病毒的基因组 genbank 文件，文件中包含：

两个基因组：LC553263.1 和 LC553262.1

一个基因组会有多个基因，下面是它的基因组结构：

1、提取单个基因CDS

main.py

from BaimoTools import BaimoTools

gb_file = f"res/genbank/SARS-CoV-2.gb"
fasta_file = f"out/output_s.fasta"
baimoTools = BaimoTools(gb_file, fasta_file)
# baimoTools.extract_cds('S')

输出文件 output_s.fasta，分别提取到两个基因组的 S 基因 CDS 区域：

2、提取多个基因CDS

main.py

from BaimoTools import BaimoTools

gb_file = f"res/genbank/SARS-CoV-2.gb"
fasta_file = f"out/output_s_m_orf10.fasta"
baimoTools = BaimoTools(gb_file, fasta_file)
baimoTools.extract_cds(['S', 'M', 'ORF10'])

输出文件 output_s_m_orf10.fasta，分别提取到两个基因组的 S，M，ORF10 基因 CDS 区域：：

2、提取全部基因CDS

main.py

from BaimoTools import BaimoTools

gb_file = f"res/genbank/SARS-CoV-2.gb"
fasta_file = f"out/output_s.fasta"
baimoTools = BaimoTools(gb_file, fasta_file)
# baimoTools.extract_cds("")

输出文件 output_all.fasta，分别提取到两个基因组的全部基因 CDS 区域：

下一步更新其他基因特征提取，及格式转换功能

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