use strict;
use warnings;

my $a = 'AYGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA';
my $b = 'ACGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTKA';

my $merged = $a;
while ($b =~ /([RYSWKMBDHV])/g) {
    my $pos = $-[0];
    substr $merged, $pos, 1, $1;
}

# $merge contains what you want

[download]

The only "unusual" thing in there is the usage of @- to get the match position.

Perl 6 - second systems done right

In reply to Re: merging dna sequences by moritz
in thread merging dna sequences by garyboyd

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