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

1 介绍

在基因结构分析或其他生物功能分析中会时常用到 CDS 序列，以及其他诸如 mRNA 序列，misc RNA序列等具有生物意义的序列片段。而NCBI 的基因库中已经包含有这些的信息，但是只有一部分是整理可下载的。而剩下的一部分可以通过 genbank给出的位点信息来提取，个人能力有限，这里只做抛转之用。下面以提取 CDS 为例，记录提取序列过程，其他特征序列类似。

2 结构目录

mark

3 Python代码

序列自动下载可以通过 Biopython 的 Entrez.efetch 方法来实现，这里以本地文件为例

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time    : 2018\9\20 0020 18:32
# @Author  : Baimoc
# @Email   : baimoc@163.com
# @File    : main.py
import os
from Bio import SeqIO


def format_fasta(ana, seq, num):
    """
    格式化文本为 fasta格式
    :param ana: 注释信息
    :param seq: 序列
    :param num: 序列换行时的字符个数
    :return: fasta格式文本
    """
    format_seq = ""
    for i, char in enumerate(seq):
        format_seq += char
        if (i + 1) % num == 0:
            format_seq += "\n"
    return ana + format_seq + "\n"


def get_cds(gb_file, f_cds):
    """
    从 genbank 文件中提取 cds 序列及其完整序列
    :param gb_file: genbank文件路径
    :param f_cds: 是否只获取一个 CDS 序列
    :return: fasta 格式的 CDS 序列， fasta 格式的完整序列 
    """
    # 提取完整序列并格式为 fasta
    gb_seq = SeqIO.read(gb_file, "genbank")
    complete_seq = str(gb_seq.seq)
    complete_ana = ">" + gb_seq.id + ":" + gb_seq.annotations["accessions"][2] + " " + gb_seq.description + "\n"
    complete_fasta = format_fasta(complete_ana, complete_seq, 70)

    # 提取 CDS 序列并格式为 fasta
    cds_num = 1
    cds_fasta = ""
    for ele in gb_seq.features:
        if ele.type == "CDS":
            cds_seq = ""
            cds_ana = ">lcl|" + gb_seq.id + "_cds_" + ele.qualifiers['protein_id'][0] + "_" + str(cds_num) + " [gene=" + \
                      ele.qualifiers['gene'][0] + "]" + \
                      " [db_xref=" + ele.qualifiers['db_xref'][0] + "]" + " [protein=" + ele.qualifiers['product'][
                          0] + "]" + \
                      " [protein_id=" + ele.qualifiers['protein_id'][0] + "]" + " [gbkey=CDS]\n"
            cds_num += 1
            for ele1 in ele.location.parts:
                cds_seq += complete_seq[ele1.start:ele1.end]
            cds_fasta += format_fasta(cds_ana, cds_seq, 70)
            if (f_cds):
                break
    return cds_fasta, complete_fasta


if __name__ == '__main__':
    # 文件输出路径
    cds_file = "out/cds.fasta"
    complete_file = "out/complete.fasta"
    # genbank 文件路径
    res_dir = "res"
    cds_file_obj = open(cds_file, "w")
    complete_file_obj = open(complete_file, "w")
    for file in os.listdir(res_dir):
        cds_fasta, complete_fasta = get_cds(res_dir + os.sep + file, #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time    : 2018\9\20 0020 18:32
# @Author  : Baimoc
# @Email   : baimoc@163.com
# @File    : main.py
import os
from Bio import SeqIO


def format_fasta(ana, seq, num):
    """
    格式化文本为 fasta格式
    :param ana: 注释信息
    :param seq: 序列
    :param num: 序列换行时的字符个数
    :return: fasta格式文本
    """
    format_seq = ""
    for i, char in enumerate(seq):
        format_seq += char
        if (i + 1) % num == 0:
            format_seq += "\n"
    return ana + format_seq + "\n"


def get_cds(gb_file, f_cds):
    """
    从 genbank 文件中提取 cds 序列及其完整序列
    :param gb_file: genbank文件路径
    :param f_cds: 是否只获取一个 CDS 序列
    :return: fasta 格式的 CDS 序列， fasta 格式的完整序列 
    """
    # 提取完整序列并格式为 fasta
    gb_seq = SeqIO.read(gb_file, "genbank")
    complete_seq = str(gb_seq.seq)
    complete_ana = ">" + gb_seq.id + ":" + gb_seq.annotations["accessions"][2] + " " + gb_seq.description + "\n"
    complete_fasta = format_fasta(complete_ana, complete_seq, 70)

    # 提取 CDS 序列并格式为 fasta
    cds_num = 1
    cds_fasta = ""
    for ele in gb_seq.features:
        if ele.type == "CDS":
            cds_seq = ""
            cds_ana = ">lcl|" + gb_seq.id + "_cds_" + ele.qualifiers['protein_id'][0] + "_" + str(cds_num) + " [gene=" + \
                      ele.qualifiers['gene'][0] + "]" + \
                      " [db_xref=" + ele.qualifiers['db_xref'][0] + "]" + " [protein=" + ele.qualifiers['product'][
                          0] + "]" + \
                      " [protein_id=" + ele.qualifiers['protein_id'][0] + "]" + " [gbkey=CDS]\n"
            cds_num += 1
            for ele1 in ele.location.parts:
                cds_seq += complete_seq[ele1.start:ele1.end]
            cds_fasta += format_fasta(cds_ana, cds_seq, 70)
            if (f_cds):
                break
    return cds_fasta, complete_fasta


if __name__ == '__main__':
    # 文件输出路径
    cds_file = "out/cds.fasta"
    complete_file = "out/complete.fasta"
    # genbank 文件路径
    res_dir = "res"
    cds_file_obj = open(cds_file, "w")
    complete_file_obj = open(complete_file, "w")
    for file in os.listdir(res_dir):
        cds_fasta, complete_fasta = get_cds(res_dir + os.sep + file, True)
        cds_file_obj.write(cds_fasta)
        complete_file_obj.write(complete_fasta)

4 其他方法获取

类型	编号
AY，AP	同一个基因存在多个提交版本时的序列编号
NC，NM	NCBI 官方推荐及使用的序列编号
IMAGE等	针对特定物种，或特定组织提供的序列编号