#!perl
use strict;
use warnings;
my @testdata = (['CCCATCTGTCCTTATTTGCTG', [qw(ATCTG ATTTG)]]
,['ACCCATCTGTCCTTGGCCAT', [qw(CCATC)]]
,['CCACCAGCACCTGTC', [qw(CCACC CCAGC GCACC)]]
,['CCCAACACCTGCTGCCT', [qw(CCAAC ACACC)]]);
for (@testdata) {
my ($str, $pats) = @$_;
print put_bracket($str, @$pats), "\n";
}
sub put_bracket
{
my $str = shift;
# Combine multiple match strings into alternations
my $rx = join '|', @_;
my @brackets;
# Store bracket points for every match
while ($str =~ /(?=($rx))/g) {
push(@brackets, [$-[0], length($1)+$-[0]]);
}
# Condense overlapping brackets
for my $i (0..$#brackets-1) {
if ($brackets[$i][1] >= $brackets[$i+1][0]) {
$brackets[$i+1][0] = $brackets[$i][0];
@{$brackets[$i]} = ();
}
}
# Apply the brackets (from back to front)
while (@brackets) {
my $b = pop @brackets;
next unless @$b;
substr($str, $b->[1], 0) = ']';
substr($str, $b->[0], 0) = '[';
}
return $str;
}
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