my $myfile= 'C:/Documents and Settings/XXX/Desktop/YYY/test.txt';

open (FILE, "$myfile") || die "Can't open '$myfile': $!\n";
my @parse = <FILE>;
close(FILE);

foreach (@parse) {
chomp;
$_ =~ s/^(gi\d+?)(\|.+?\|.+?\|)\s+?(.+?)/$1 ($2) $3/g;