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 and sysread.

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 $sequence;
my $read = sysread $fh, $sequence, $length;
die "Failed to read $length bytes from $input, got $read"
  if $length != $read;
[download]

Now $sequence 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.

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.