Perhaps you just need to use substr

#!/usr/bin/perl 
use warnings;
use strict; 
use Bio::DB::GenBank;
use Bio::SeqIO;  

my $acc = "NC_027152.1"; 
my $gb  = new Bio::DB::GenBank;
my $seq1 = $gb->get_Seq_by_acc($acc);
my $sequence = $seq1->seq; 
region($sequence,313,1374);

sub region {
  my ($string,$begin,$end) = @_;
  my $length = $end - $begin + 1;
  my $region =  lc substr($string,$begin-1,$length);
 
  my @line;
  my $posn = 1;
  print "Posn $begin - $end length $length\n";
  while ($region =~ /(.{10}|.{1,9}$)/g){
    push @line,$1;
    if (@line == 6){
      printf "%4d %s\n",$posn,join ' ',@line;
      $posn += @line * 10;
      @line=();
    }
  }
  printf "%4d %s\n",$posn,join ' ',@line if (@line);
}

[download]
poj

In reply to Re: How to retrieve the intergenic sequences and the introns from GenBank page of NCBI? by poj
in thread How to retrieve the intergenic sequences and the introns from GenBank page of NCBI? by supriyoch_2008

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