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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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HXCOPY(1)							  HTML-XML-utils							 HXCOPY(1)

NAME
hxcopy - copy an HTML file and update its relative links SYNOPSIS
hxcopy [ -i old-URL ] [ -o new-URL ] [ file-or-URL [ file-or-URL ] ] DESCRIPTION
The hxcopy command copies its first argument to its second argument, while updating relative links. The input is assumed to be HTML or XHTML and may be slightly reformatted in the process. If the second argument is omitted, hxcopy writes to standard output. In this case the option -o is required. If the first argument is also omitted, hxcopy reads from standard input. In this case the option -i is required. OPTIONS
The following options are supported: -i old-URL For the purposes of updating relative links, act as if old-URL is the location from which the input is copied. If this option is omitted, the actual location of the first argument is used for calculating relative links. -o new-URL For the purposed of updating relative links, act as if new-URL is the location to which the input is copied. If this option is omitted, the actual location of the second argument is used for calculating relative links. ENVIRONMENT
To use a proxy to retrieve remote files, set the environment variables http_proxy and ftp_proxy. E.g., http_proxy="http://localhost:8080/" BUGS
Unlike the last argument of cp(1), the last argument of hxcopy must be a file, not a directory. The second argument must be a local file. Writing to a URL is not yet implemented. To work around this, replace hxcopy file.html http://example.org/file.html by hxcopy -o http://example.org/file.html file.html tmp.html and then upload tmp.html to the given URL with some other command, such as curl(1). The first argument, however, may be a URL. hxcopy will download the given file. (Currently only HTTP is supported.) EXAMPLE
Assume the HTML file foo.html contains a relative link to "../bar.html". Here are some examples of commands: hxcopy foo.html bar/foo.html The file foo.html is copied to ../bar/foo.html and the relative link to "../bar.html" becomes "../../bar.html". hxcopy foo.html ../foo.html The file foo.html is copied to ../foo.html and the relative link to "../bar.html" is rewritten as "bar.html". hxcopy -i http://my.org/dir1/foo.html -o http://my.org/foo.html file1.html file2.html The file file1.html is copied to file2.html and the relative link to "../bar.html" is rewritten as "bar.html". A command like this may be useful to update files that are later uploaded to a server. SEE ALSO
cp(1), curl(1), hxwls(1) 6.x 9 Dec 2008 HXCOPY(1)
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