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use strict;
use warnings;
...
    my $skew = 100 * $slew / $file1Hash{$item};
    printf "%s,%d,%.8f\n", $line, $file1Hash{$item}, $skew;
}

$ perl -e 'use strict;
> use warnings;
...
dt_pp50,0,0,2,0.000,0.000,0,0.000,200,0.00000000
er_tk02,0,2,3,0.002,0.004,0,0.001,305,0.00065473
ef_yb41,0,1,5,0.000,0.000,0,0.000,200,0.00000000