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Top Forums Shell Programming and Scripting Transpose columns to Rows : Big data Post 302443633 by genehunter on Monday 9th of August 2010 04:44:05 PM
Old 08-09-2010
Transpose columns to Rows : Big data

Hi,
I did read a few posts on the subjects, tried out a few solutions, but did not solve my problem.
https://www.unix.com/302121568-post11.html
https://www.unix.com/shell-programmin...ows-etc-4.html

Please help. Problem very similar to the second link poster, but slighlt different input format. The field separator is space . The actual data matrix is a file with 2000 rows and 600,000 columns.
Input style:
Code:
IID    PAT    MAT    SEX    PHENOTYPE    rs15286_1    rs319_1    rs80300_1    rs40777_1    rs8597_1    rs5136_1    rs60595_1    rs64968_1    rs4405_1    rs1554_1
TD-MIKV    0 0 2 1 1 0 0 1 0 1 0 1 1 0
TD-HA4Q 0 0 2 1 1 0 0 0 0 0 0 0 0 0
TD-H9ZG 0 0 2 2 0 0 0 1 0 0 0 0 0 0
TD-HAQX 0 0 2 1 0 0 0 2 0 0 0 0 0 0
TD-HA5E 0 0 2 2 0 1 1 1 0 0 0 1 1 0
TD-MGFV 0 0 2 2 1 0 0 0 0 NA 0 0 0 1
TD-HB4V 0 0 2 1 0 0 1 0 1 NA 0 1 1 0
TD-MIPE 0 0 2 2 0 0 0 1 0 0 0 0 0 0
TD-MINR 0 0 2 2 0 0 0 0 0 2 0 1 1 0

Output style
Code:
   IID TD-MIKV TD-HA4Q TD-H9ZG TD-HAQX TD-HA5E TD-MGFV TD-HB4V TD-MIPE TD-MINR
PAT 0 0 0 0 0 0 0 0 0
MAT 0 0 0 0 0 0 0 0 0
SEX 2 2 2 2 2 2 2 2 2
PHENOTYPE 1 1 2 1 2 2 1 2 2
rs15286_1 1 1 0 0 0 1 0 0 0
rs319_1 0 0 0 0 1 0 0 0 0
rs80300_1 0 0 0 0 1 0 1 0 0
rs40777_1 1 0 1 2 1 0 0 1 0
rs8597_1 0 0 0 0 0 0 1 0 0
rs5136_1 1 0 0 0 0 NA NA 0 2
rs60595_1 0 0 0 0 0 0 0 0 0
rs64968_1 1 0 0 0 1 0 1 0 1
rs4405_1 1 0 0 0 1 0 1 0 1
rs1554_1 0 0 0 0 0 1 0 0 0

awk or python preferable, since I understand them a teeny weeny bit.
Thanks in advance,
Regards
~GH
 

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IO::All::HTTP(3pm)					User Contributed Perl Documentation					IO::All::HTTP(3pm)

NAME
IO::All::LWP - Extends IO::All to HTTP URLs SYNOPSIS
use IO::All; $content < io('http://example.org'); # GET webpage into scalar io('http://example.org') > io('index.html'); # GET to file "hello " > io('http://example.org/index.html'); # PUT webpage # two ways of getting a page with a password: $content < io('http://me:secret@example.org'); $content < io('http://example.org')->user('me')->password('secret'); DESCRIPTION
This module extends IO::All for dealing with HTTP URLs. Note that you don't need to use it explicitly, as it is autoloaded by IO::All whenever it sees something that looks like an HTTP URL. The SYNOPSIS shows some simple typical examples, but there are many other interesting combinations with other IO::All features! For example, you can get an HTTP URL and write the content to a socket, or to an FTP URL, of to a DBM file. METHODS
This is a subclass of IO::All::LWP. The only new method is "http", which can be used to create a blank IO::All::HTTP object; or it can also take an HTTP URL as a parameter. Note that in most cases it is simpler just to call io('http://example.com'), which calls the "http" method automatically. OPERATOR OVERLOADING
The same operators from IO::All may be used. < GETs an HTTP URL; > PUTs to an HTTP URL. SEE ALSO
IO::All, IO::All::LWP, LWP. AUTHORS
Ivan Tubert-Brohman <itub@cpan.org> and Brian Ingerson <ingy@cpan.org> COPYRIGHT
Copyright (c) 2007. Ivan Tubert-Brohman and Brian Ingerson. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See <http://www.perl.com/perl/misc/Artistic.html> perl v5.10.0 2007-03-29 IO::All::HTTP(3pm)
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