Alternatively, Is it possible to look at the values of a hash and find out how many times my search string is present? 
#input = $search
    foreach my $key (keys %hash) {
        $searchline = $hash{$key};
        if ($searchline =~ /$search/gi) {
        $contains ++;
        }
        }

[download]
Because this seems also to stop counting once it finds the FIRST $search, making the resulting "$contains" merely equal to the number of values that happen to contain at least one of the $search strings....

In reply to Re^3: FASTA riddle. by MaroonBalloon
in thread FASTA riddle. by MaroonBalloon

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