I think your problem is
- you have a large file
- you have created a new file with line endings removed
- now you want to read in characters between two positions in the new file
To do that you can use sysseek
use Fcntl qw(SEEK_SET);
my $input = '...';
my $start = 1_490_117;
my $end = 1_492_312;
my $length = $end - $start +1;
open my $fh, '<', $input or die "Can't open $input: $!";
sysseek($fh, $start, SEEK_SET) or die "Can't seek to $start in $input:
my $read = sysread $fh, $sequence, $length;
die "Failed to read $length bytes from $input, got $read"
if $length != $read;
will contain the DNA sequence from 1,490,117 to 1,492,312 including both end points.
Note: sysread and sysseek use unbuffered IO, don't mix calls to them on a filehandle using other functions such as read, <> or eof.