python学习——通过命令行参数根据fasta文件中染色体id提取染色体序列

 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‘)))

1 (base) e:\15_python\DEBUG>python GetSeqFromChrID.py -i genome_test.fa -o chr14.fa chr14