OK not shortest :-/ but fastest :-), vis:

print "Writing file...\n";
open FILE, ">test.txt" or die $!;
my $line = join "\t", (1..1000);
print FILE $line, "\n" for (1..600);
close FILE;
print "File written!\n";

# Original method
open PROFILES, "<test.txt" or die $!;
my @matrix = ();
my $start = time;
while (<PROFILES>) {
 @profile = split (/\t/, $_);
 while ($j <= $#profile) {
  $matrix[$j]->[$i] = $profile[$i];
  $j++;
 }
 $i++;
 $j = 0;
}
print "Original method takes ", time-$start, " seconds\n";
close PROFILES;

# my method
open PROFILES, "<test.txt" or die $!;
@matrix = ();
$start = time;
while(<PROFILES>){
    push @matrix, [split"\t"];
}
print "My method takes ", time-$start, " seconds\n";
close PROFILES;

# Blakem's method
open PROFILES, "<test.txt" or die $!;
@matrix = ();
$start = time;
@matrix = map[split],<PROFILES>;
print "Blakem's method takes ", time-$start, " seconds\n";
close PROFILES;

__DATA__
C:\>perl matrix.pl
Writing file...
File written!
Original method takes 18 seconds
My method takes 7 seconds
Blakem's method takes 52 seconds
[download]

PS I slightly modified the original code to remove the infinite loop so it actually will work to test it.

cheers

tachyon

s&&rsenoyhcatreve&&&s&n.+t&"$'$`$\"$\&"&ee&&y&srve&&d&&print

Minor nitpick....


@row = split;
[download]

Will be different than:

@row = split /\t/;
[download]

The latter leaving the trailing newline on the last column. May or may not cause grief depending on what you do to the final matrix before trying to print it out.

Well, I never said it was fast or memory efficient. ;-) My first golfed attempt (which had a couple extra chars over the one I posted) performs much better...

push@matrix,[split]for<PROFILES>;
[download]

-Blake