Hi,
I have two strings that I want to compute the number of mismatches between
them. These two strings are of the "same" size. Let's call them 'source' string
and 'target' string. Now, the problem is that the 'source' and 'target' string
may come in ambiguous form, meaning that in one position they may contain more
than 1 (upto 4) characters. The ambiguous position is marked with square
bracketed [ATCG] region.
The example is as follows:
Example 1 (where the source is ambiguous):
my $source1 = '[TCG]GGGG[AT]'; # ambiguous
my $target1 = 'AGGGGC'; # No of mismatch = 2 on position 1 and 6
my $target2 = 'TGGGGC'; # No of mismatch = 1 on position 6 only
Example 2 (where the source is NOT ambiguous):
my $source2 = 'TGGGGT'; # not-ambiguous
my $target1 = 'AGGGGC'; # No of mismatch = 2 on position 1 and 6
my $target3 = 'TGGGGT'; # No of mismatch = 0 all position matches
Example 3 (where both source and target are ambiguous)
my $source1 = '[TCG]GGGG[AT]'; # ambiguous
my $target1 = 'AGGGG[CT]'; # ambiguous, no of mismatch = 1 only at
position 1
For example I can use bitwise operator to do it.
I have no problem when dealing with Example 1 and 2 above.
But I'm stuck with example 3, where both source and target is ambiguous.
Here is the current snippet I have, which doesn't do the job:
__BEGIN__
sub mismatches {
my($source, $target) = @_;
my @sparts = ($source =~ /(\[.*?\]|.)/g);
my @tparts = ($target =~ /(\[.*?\]|.)/g);
scalar grep $tparts[$_] !~ /^$sparts[$_]/, 0 .. $#sparts;
}
__END__
Where did I go wrong? I humbly seek advice.
Regards
Edward WIJAYA
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