To insert a literal string into a pattern you can use \Q and \E. This insures that any characters that have special meaning in a regex will be escaped and treated as literals.

As for finding all overlapping patterns, see the documentation of pos and the 0 length lookahead operator in perlre. Using pos, 0 length lookahead regexes (look for (?=) might be preferable since the documentation says that (?{...}) is experimental.

use strict;
use warnings;

my $sequence = "GGGGGGGAGAAAAAAAAAAAAAAAGAAGGA";

sub tryPattern {
  my $pattern = shift;
  my $iCount = 0;
  while ($sequence =~ /(?=\Q$pattern\E)/g) {
    $iCount++;
    my $iPos = pos($sequence);
    my $sMatch = substr($sequence, $iPos, 5);
    print "$iPos: $sMatch\n";
    pos($sequence) = $iPos + 1;
  }
  print "total found: $iCount\n";
}

tryPattern($_) foreach qw(AAAAA GGGGG GGAGA GAAGG);

[download]

Best, beth

In reply to Re: Regex KungFu help needed by ELISHEVA
in thread Regex KungFu help needed by drblove27

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.