提取fasta文件genome_test.fa中第14号染色体的序列，其内容如下：
>chr1 ATATATATAT >chr2 ATATATATATCGCGCGCGCG >chr3 ATATATATATCGCGCGCGCGATATATATAT >chr4 ATATATATATCGCGCGCGCGATATATATATCGCGCGCGCG >chr5 ATATATATATCGCGCGCGCGATATATATATCGCGCGCGCGATATATATAT >chr6 ATCGATGCAGCATG >chr7 TATCGCGCGCGCGATATAT >chr8 ATATCGCGCGCGCGATATATATATCGCG >chr9 ATCGCGCGCGCGATATATATATCGCG >chr10 GCGCGCGATATAT >chr11 CGCGATATATATATC >chr12 ATATATCGCGCGCGCGATATAT >chr13 ATATATCGCGCGCGCGATATATGCGATATATATATC >chr15 ATATATGCGAT >chr14 GCGCGCGCGATATATGCGAT >chr16 GCGATATATGCGATATATATATC >chr17 GCGCGCGCGATATATATATCGCGCGCGCGATATATATAT >chr18 GCGCGCGCGATATATATATCGCGCGCGCGATATATATATATATGCGATATATATATC >chr19 ATATGCGATATATATATCGCGCGCGCGATATATATATCGCGCGCGCGATATATATATATATGCGA >chr20 TATGCGATATATATATCGCGCGCGCGATATATATATCGCGCGCGCGATATATATATATATGCGA >chr21 TATATCGCGCGCGCGATATATATATCGCGCGCGCGATATATATATATATGCGA >chr22 ATATATATCGCGCGCGCGATATATATATATATGCGA >chrX CGCGCGCGATATATATATATATGCGA >chrY CGCGCGCGATATATATATATATGCGACGCGCGCGATATATATATATATGCGACGCGCGCGATATATATATATATGCGA
用python以及命令行参数实现
新建.py文件“”GetSeqFromChrID.py”，
python脚本如下：
1 import argparse
2
3 def read_fasta(input):
4
5 with open(input, ‘r‘) as f:
6 fasta = {}
7 for line in f:
8 line = line.strip()
9 if line[0] == ‘>‘:
10 header = line[1:]
11 else:
12 sequence = line
13 fasta[header] = fasta.get(header, ‘‘) + sequence
14
15 return fasta
16
17
18 if __name__ == ‘__main__‘:
19 # read arguments
20 parser = argparse.ArgumentParser(description="this program is used to extract a single "
21 "sequence from genome")
22 parser.add_argument(‘--input‘, ‘-i‘,
23 type=str,
24 help=‘input file in fasta format‘)
25 parser.add_argument(‘--output‘, ‘-o‘,
26 type=str,
27 help=‘output file‘)
28 parser.add_argument(‘seq_id‘,
29 type=str,
30 help=‘sequence id‘)
31 args = parser.parse_args()
32
33 fasta = read_fasta(args.input)
34 with open(args.output, ‘w‘) as f:
35 f.write(‘>{:s}\n{:s}\n‘.format(args.seq_id,fasta.get(args.seq_id, ‘can not found this sequence‘)))
命令行参数输入如下：红色字体是输入部分
1 (base) e:\15_python\DEBUG>python GetSeqFromChrID.py -i genome_test.fa -o chr14.fa chr14
结果如下：
原文地址：https://www.cnblogs.com/caicai2019/p/10867405.html
时间： 2024-10-08 13:53:13