根据位置信息提取 fasta 文件中的序列 -- extract fasta sequence by their position

#!/usr/bin/env python

# usages: python extract_seq_by_pos.py input.fasta id_start_end > result.fasta

import sys

import re

FASTA= sys.argv[1]

BED= sys.argv[2]

fasta= open(FASTA, 'U')

fasta_dict= {}

for line in fasta:

    line= line.strip()

    if line == '':

        continue

    if line.startswith('>'):

        seqname= line.lstrip('>')

        seqname= re.sub('\..*', '', seqname)

        fasta_dict[seqname]= ''

    else:

        fasta_dict[seqname] += line

fasta.close()

bed= open(BED, 'U')

for line in bed:

    line= line.strip().split('\t')

    outname= line[0] + ':' + line[1] + '-' + line[2]

    print('>' + outname)

    s= int(line[1])-1

    e= int(line[2])-1

    print(fasta_dict[line[0]][s:e])

bed.close()

sys.exit()