使用Python脚本提取基因组指定位置序列

#下列内容保存到list.txt
gene46   NC_000964.3  42917  43660   
NP_387934.1  NC_000964.3    59504  60070     
yfmC  NC_000964.3  825787   826734  -
cds821  NC_000964.3  885844  886173 -

# -*- coding: utf-8 -*-
#初始传递命令
input_file = 'Bacillus_subtilis.str168.fasta'
list_file = 'list.txt'
output_file = 'gene.fasta'
name_detail = True
##读取文件
#读取基因组序列
seq_file = {}
with open(input_file, 'r') as input_fasta:
    for line in input_fasta:
        line = line.strip()
        if line[0] == '>':
            seq_id = line.split()[0]
            seq_file[seq_id] = ''
        else:
            seq_file[seq_id]  = line
input_fasta.close()
#读取列表文件
list_dict = {}
with open(list_file, 'r') as list_table:
    for line in list_table:
        if line.strip():
            line = line.strip().split('\t')
            list_dict[line[0]] = [line[1], int(line[2]) - 1, int(line[3]), line[4]]
list_table.close()
##截取序列并输出
#定义函数，用于截取反向互补
def rev(seq):
    base_trans = {'A':'T', 'C':'G', 'T':'A', 'G':'C', 'N':'N', 'a':'t', 'c':'g', 't':'a', 'g':'c', 'n':'n'}
    rev_seq = list(reversed(seq))
    rev_seq_list = [base_trans[k] for k in rev_seq]
    rev_seq = ''.join(rev_seq_list)
    return(rev_seq)
#截取序列并输出
output_fasta = open(output_file, 'w')
for key,value in list_dict.items():
    if name_detail:
        print('>'   key, '['   value[0], value[1]   1, value[2], value[3]   ']', file = output_fasta)
    else:
        print('>'   key, file = output_fasta)
    seq = seq_file['>'   value[0]][value[1]:value[2]]
    if value[3] == ' ':
        print(seq, file = output_fasta)
    elif value[3] == '-':
        seq = rev(seq)
        print(seq, file = output_fasta)
output_fasta.close()</pre>

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#导入模块，初始传递命令、变量等
import argparse
parser = argparse.ArgumentParser(description = '\n该脚本用于在基因组特定位置截取序列，需额外输入记录有截取序列信息的列表文件', add_help = False, usage = '\npython3 seq_select.py -i [input.fasta] -o [output.fasta] -l [list]\npython3 seq_select.py --input [input.fasta] --output [output.fasta] --list [list]')
required = parser.add_argument_group('必选项')
optional = parser.add_argument_group('可选项')
required.add_argument('-i', '--input', metavar = '[input.fasta]', help = '输入文件，fasta 格式', required = True)
required.add_argument('-o', '--output', metavar = '[output.fasta]', help = '输出文件，fasta 格式', required = True)
required.add_argument('-l', '--list', metavar = '[list]', help = '记录“新序列名称/序列所在原序列ID/序列起始位置/序列终止位置/正链（ ）或负链（-）”的文件，以 tab 作为分隔', required = True)
optional.add_argument('--detail', action = 'store_true', help = '若该参数存在，则在输出 fasta 的每条序列 id 中展示序列在原 fasta 中的位置信息', required = False)
optional.add_argument('-h', '--help', action = 'help', help = '帮助信息')
args = parser.parse_args()
##读取文件
#读取基因组序列
seq_file = {}
with open(args.input, 'r') as input_fasta:
    for line in input_fasta:
        line = line.strip()
        if line[0] == '>':
            seq_id = line.split()[0]
            seq_file[seq_id] = ''
        else:
            seq_file[seq_id]  = line
input_fasta.close()
#读取列表文件
list_dict = {}
with open(args.list, 'r') as list_file:
    for line in list_file:
        if line.strip():
            line = line.strip().split('\t')
            list_dict[line[0]] = [line[1], int(line[2]) - 1, int(line[3]), line[4]]
list_file.close()
##截取序列并输出
#定义函数，用于截取反向互补
def rev(seq):
    base_trans = {'A':'T', 'C':'G', 'T':'A', 'G':'C', 'a':'t', 'c':'g', 't':'a', 'g':'c'}
    rev_seq = list(reversed(seq))
    rev_seq_list = [base_trans[k] for k in rev_seq]
    rev_seq = ''.join(rev_seq_list)
    return(rev_seq)
#截取序列并输出
output_fasta = open(args.output, 'w')
for key,value in list_dict.items():
    if args.detail:
        print('>'   key, '['   value[0], value[1]   1, value[2], value[3]   ']', file = output_fasta)
    else:
        print('>'   key, file = output_fasta)
    seq = seq_file['>'   value[0]][value[1]:value[2]]
    if value[3] == ' ':
        print(seq, file = output_fasta)
    elif value[3] == '-':
        seq = rev(seq)
        print(seq, file = output_fasta)
output_fasta.close()

#python3 seq_select.py -h
python3 seq_select.py -i Bacillus_subtilis.str168.fasta -l list.txt -o gene.fasta --detail