Is this what you want, it flips on the diagonal? The main requirement is that you have as much free disk space for the temp files as the total file size. You will be limited in the number of columns you can transpose by the number of open file descriptors your Perl will let you have. It is very easy to hack the logic to do N colunms per pass at the expense of 1 full read of the input file per extra pass. Alternatively you could DBM or tie a hash to a file and use the keys as pseudo file handles and just append data to the values. Although there is more I/O with a multipass approach is is very vanilla I/O which perl does really fast.

Update

See this article for info on how to up the number of available file descriptors (probably 1024/process) on a Linux based system. No idea how it is dealt with on other systems.

It should be really fast as we make a single pass through the input data and then effectively just write it out (each temp file has one full line in it). 

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 $t
+mp$_ $!\n";
        print {$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:\>

[download]

cheers

tachyon

In reply to Re: Re:^2 Binary file handling by tachyon
in thread Binary file handling by Hena

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