OK, here's my first attempt at a solution

#my $old_seq='ATGC---ACGT---TAGCAAGGTAAAT';
#my $new_seq='----AT-GC----ACGT----TAGCAA----------GGTAAAT---';
print "old seq is\n$old_seq\nnew seq is\n$new_seq\n";

my @old_array = split //, lc ($old_seq);
my @new_array = split //, lc ($new_seq);


my $n_old=0;
my $n_new=0;
my %gaps;
while (my $old_base = shift @old_array){


my $new_base = shift @new_array;
#print "base in oldseq is $old_base, base in newseq is $new_base\n";



if ($old_base eq $new_base){
#    print "match!\n";
    $n_old++;
    $n_new++;
    next;
}
else{
#    print "no match! - must be a new gap at position $n_new new, $n_o
+ld old\n";
    my $new_gap_length=0;
    while ($new_base = shift @new_array){
        $n_new++;
        $new_gap_length++;
#        print "newbase is $new_base\n";
        if ($new_base eq $old_base){
#            print "found it - length was $new_gap_length\n";
            $gaps{$n_new-$new_gap_length} = $new_gap_length;
            $n_old++;
            $n_new++;
            last;
        }
        
    }
}
}

foreach (sort {$a <=> $b} keys %gaps){
print "gap at position in new $_, length $gaps{$_}\n";
}

[download]
It always reports the new gap as being at the end of the existing gap in the cases where the new gap's position can't be unambiguously decided. Anyone spot any flaws in this?

In reply to Re: finding substrings that have been inserted into a string by Anonymous Monk
in thread finding substrings that have been inserted into a string by Anonymous Monk

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