open IN, "<file1" or die $!;
while(<IN>){
        $sID{$1} = 1 if /^(\w+)\t/;
}
close IN;

open IN, "<file2" or die $!;
map {$i++; push @cols, $i-1 if exists $sID{$_}} split(/\t|$/, <IN>);
while(@a = split /\t|$/, <IN>){
        print join "\t", @a[@cols],"\n";
}
close IN;