Obtain 15 characters from a string that contain less than 15 characters in Perl - perl

Question

I have a sequence and a number representing the location of a residue(character). I want to take 7 residues from each side of the residue. This is the code to do that:
my $seq = substr($sequence, $location-8, 14);
This grabs 7 from each side of the residue. However, there are some sequences where there is less than 7 residues on either side. So when this occurs, I get an error saying:
substr outside of string at test9.pl line 52 (#1) (W substr)(F) You tried to reference a substr() that pointed outside of a string. That is, the absolute value of the offset was larger than the length of the string.
How can I change the empty places and replace them with another letter (X for example).
For example, if there is a sequence
ABCDEFGH
and $location points to D, I need 7 on each side so the result would be:
XXXXABCDEFGHXXX

Answer 1

Expanding on my comment above. I would create a my_substr function that encapsulates the padding and location shift.
my $sequence = "ABCDEFGH";
my $location = 3;
sub my_substr {
my ($seq, $location, $pad_length) = #_;
my $pad = "X"x$pad_length;
return substr("$pad$seq$pad", $location, (2*$pad_length+1));
}
print my_substr($sequence, $location, 7) . "\n";
yields
XXXXABCDEFGHXXX

Answer 2

This is an very verbose answer, but more or less gets you what you want:
use strict;
use warnings;
my $sequence = 'ABCDEFGH';
my $wings = 7;
my $location = index $sequence, 'D';
die "D not found" if $location == -1;
my $start = $location - $wings;
my $length = 1 + 2 * $wings;
my $leftpad = 0;
if ($start < 0) {
$leftpad = -1 * $start;
$start = 0;
}
my $seq = substr($sequence, $start, $length);
$seq = ('X' x $leftpad) . $seq if $leftpad;
my $rightpad = $length - length ($seq);
$seq .= 'X' x $rightpad if $rightpad > 0;
print $seq;
Or to avoid all the extra work, could just create a new $sequence variable containing padding:
my $sequence = 'ABCDEFGH';
my $wings = 7;
my $location = index $sequence, 'D';
die "D not found" if $location == -1;
my $paddedseq = ('X' x $wings) . $sequence . ('X' x $wings);
my $seq = substr($paddedseq, $location, 1 + 2 * $wings);
print $seq;