Rather than inserting the brackets as the substrings are found, you could keep track of the indicies of the substrings, filter out interior indicies for overlapping substrings, then insert the brackets at the remaining indicies.

Lessee... somthing like...

#!/usr/bin/perl -w
use strict;

my $s1 ='CCCATCTGTCCTTATTTGCTG';  my @a1 = qw(ATCTG ATTTG);
my $s2 ='ACCCATCTGTCCTTGGCCAT';   my @a2 = qw(CCATC);
my $s3 ='CCACCAGCACCTGTC';        my @a3 = qw(CCACC CCAGC GCACC);
my $s4 ='CCCAACACCTGCTGCCT';      my @a4 = qw(CCAAC ACACC);

put_bracket($s1,\@a1);
put_bracket($s2,\@a2);

put_bracket($s3,\@a3);
put_bracket($s4,\@a4);

sub put_bracket
{
    my  ($str,$ar) = @_;
    my  $slen = length $ar->[0];
    my  @brackets;
    foreach my $subs ( @$ar  )
    {
        my $idx  = index($str,$subs);
        my $bgn = $idx;
        my $end = $idx + $slen + 1;
        push @brackets, ($bgn, $end);
    }
    
    my @filtered = $brackets[0];
    for (1..$#brackets-1)
    {
        push @filtered, $brackets[$_] if 
        ($brackets[$_] < $brackets[$_+1] and
        $brackets[$_-1] < $brackets[$_]);
    }
    push @filtered, $brackets[-1];
    while (@filtered)
    {
        substr($str, pop @filtered, 0, ']');
        substr($str, pop @filtered, 0, '[');
    }
    print $str,"\n";
    return;
}

[download]

Edit: Note that the above could return some incorrect brackets if all of the substrings are not the same length. It is probably moot though, as I see you assume that all of the substrings are the same length in your original example

In reply to Re: Bracketing Substring(s) in the String by thundergnat
in thread Bracketing Substring(s) in the String by monkfan

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • 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! —
  • 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:
    & &amp;
    < &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.