script to get certain nucleotide from within a specific contig from a fasta file

export_nuc_from_fasta.py

#!/usr/bin/env python

import anvio.utils as u
import argparse
import sys
parser =  argparse.ArgumentParser(description='Get nucleotides from fasta file beyween user defined nucleotide positions inside a specified contig')
parser.add_argument('-1','--N1',metavar='INT',dest='n1',type=int,help='Nucleotide sequence start position')
parser.add_argument('-2','--N2',metavar='INT',dest='n2',type=int,help='Nucleotide sequence start position')
parser.add_argument('-c','--contig',metavar='STRING',dest='c',help='Contig name')
parser.add_argument('-o','--out',metavar='FILE',dest='output',help='Output file')
parser.add_argument('-i','--input',metavar='FILE',dest='input',help='Input file')
args = parser.parse_args()

f = u.get_FASTA_file_as_dictionary(args.input)

with open(args.output,'w') as o:
	o.write(">%s_nucleotide_range_%s_to_%s\n"%(args.c,args.n1,args.n2))
	o.write(f[args.c][args.n1:args.n2])