C:\>type transpose.pl
#!/usr/bin/perl -w
use strict;
transpose90( "c:/data.txt", "c:/data-transpose.txt" );

sub transpose90 {
    my ( $infile, $outfile, $tmp ) = @_;
    $tmp ||= 'c:/tmp/temp';
    open IN, $infile or die "Can't read $infile $!\n";
    # find number of columns and open a temp file for each
    local $_ = <IN>;
    chomp;
    my @data = split ' ';
    my $num_cols = $#data;
    my @fhs;
    for( 0..$num_cols ) {
        open $fhs[$_], ">$tmp$_.txt" or die "Can't create temp file $tmp$_ $!\n";
        print {$fhs[$_]} $data[$_], "\t";
    }
    while( <IN> ) {
        chomp;
        @data = split ' ';
        print {$fhs[$_]} $data[$_], "\t" for 0..$num_cols;
    }
    close IN;
    open OUT, ">$outfile" or die "Can't write $outfile $!\n";
    for ( 0.. $num_cols ) {
        close $fhs[$_]; # close the temp file
        open IN, "$tmp$_.txt" or die "Can't read temp file $tmp$_ $!\n";
        print OUT scalar(<IN>), "\n";
        close IN;
        unlink "$tmp$_.txt"
    }
    close OUT;
}


C:\>type data.txt
11      12      13
21      22      23
31      32      33

C:\>transpose.pl

C:\>type data-transpose.txt
11      21      31
12      22      32
13      23      33

C:\>