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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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JIGDO-LITE(1)															     JIGDO-LITE(1)

NAME
jigdo-lite - Download jigdo files using wget SYNOPSIS
jigdo-lite [ URL ] DESCRIPTION
See jigdo-file(1) for an introduction to Jigsaw Download. Given the URL of a `.jigdo' file, jigdo-lite downloads the large file (e.g. a CD image) that has been made available through that URL. wget(1) is used to download the necessary pieces of administrative data (contained in the `.jigdo' file and a corresponding `.template' file) as well as the many pieces that the large file is made from. The jigdo-file(1) utility is used to reconstruct the large file from the pieces. `.jigdo' files that contain references to Debian mirrors are treated specially: When such a file is recognized, you are asked to select one mirror out of a list of all Debian mirrors. If URL is not given on the command line, the script prompts for a location to download the `.jigdo' file from. The following command line options are recognized: -h --help Output short summary of command syntax. -v --version Output version number. --scan FILES Do not ask for "Files to scan", use this path. --noask Do not ask any questions, instead behave as if the user had pressed Return at all prompts. This can be useful when running jigdo- lite from cron jobs or in other non-interactive environments. SEE ALSO
jigdo-file(1), jigdo-mirror(1), wget(1) (or `info wget') CD images for Debian Linux can be downloaded with jigdo <URL:http://www.debian.org/CD/jigdo-cd/>. AUTHOR
Jigsaw Download <URL:http://atterer.net/jigdo/> was written by Richard Atterer <jigdo atterer.net>, to make downloading of CD ROM images for the Debian Linux distribution more convenient. 19 May 2006 JIGDO-LITE(1)
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