#! perl -slw
use strict;

# Read the file, split into fields, discard the first 2
# join fields 2/3 as required for output.

my @data = map{ join '/', (split ' ')[2,3] } <DATA>;

my @lines; # Array in which to accumulate the output.

# build each output line

for my $line ( 0 .. 2 ) { # 0 .. 89 in your app

	# by steping through the input and appending every nth element to the output

	for my $col ( 0 .. 33 ) { # 0 .. 300 in your app

		$lines[ $line ] .= $data[ $line * 34 + $col ] . ' ';
	}
}

# display the output.
print for @lines;


##</code><code>##

__DATA__
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A
000217 P015 A G
000217 P016 A G
000217 P008 N N
000217 P009 G G
000217 P010 A A
000217 P011 A G
000217 P012 A A
000217 P013 A G
000217 P014 A A

##</code><code>##

P:\test>junk
N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A
N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A
N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A A/G A/G N/N G/G A/A A/G A/A A/G A/A