while (<>) {
  my @params = split /\s*,\s*/;
  foreach my $param (@params) {
    $param =~ /(Identities|Positives|Negatives)\s+=\s+(.+)\s+\((.+)\%\)/;
    # $1 now contains which type you matched, $2 and $3 are the submatches, do what you will with them
  }
}

##</code><code>##

while (<>) {
  my %params = map {
    my ($k,$v) = split /\s*=\s*/;
    $v =~ /(.+)\s+\((.+)\%\)/;
    ($k => [$1,$2])
  } split /\s,\s*/;
}