Hi,
I am trying to put the bracket in a string given the set of its substrings. Like this: 
    String               Substrings          Desired Result
1.CCCATCTGTCCTTATTTGCTG  ATCTG ATTTG        CCC[ATCTG]TCCTT[ATTTG]CTG
2.ACCCATCTGTCCTTGGCCAT   CCATC              AC[CCATC]TGTCCTTGGCCAT
3.CCACCAGCACCTGTC        CCACC CCAGC GCACC  [CCACCAGCACC]TGTC   *
4.CCCAACACCTGCTGCCT      CCAAC ACACC        C[CCAACACC]TGCTGCCT *

[download]
My code here does the job, but only for the first two cases (where the substrings don't overlap in the string). It fails to deal with case 3 and 4 (marked with asterisks *).
#!/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);

#These two work fine.
put_bracket($s1,\@a1);
put_bracket($s2,\@a2);

#But these two don't work
put_bracket($s3,\@a3);
put_bracket($s4,\@a4);

sub put_bracket
{
    my    ($str,$ar)    = @_;
    my  $bstr;
    my  $slen = length $ar->[0];

    foreach my $subs ( @$ar  )
    {
      my $idx  = index($str,$subs);
      my $bgn = $idx;
      my $end = $idx+$slen+1;
      substr($str,$bgn,0,"[");
      substr($str,$end,0,"]");
    }
      print "$str\n";
    return ;
}

[download]

How can I resolve this problem? Am I approaching the problem correctly in the first place? I humbly seek your advice.

Regards,
Edward

In reply to 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.