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Full Discussion: Modify text file using awk
Top Forums Shell Programming and Scripting Modify text file using awk Post 302811183 by mehar on Thursday 23rd of May 2013 07:42:38 AM
Old 05-23-2013
The previous solution

Quote:
awk '{n=split ($8,TMP,";"); $8=""; for (i=1; i<=n; i++) if (match (TMP[i], /^DP=|^MQ=|^resource.EFF/)) {sub (/^.*=/,"",TMP[i]); $8=$8 ($8?"\t":"") TMP[i]}}1' FS="\t" file
gives the output as

Quote:
chr1 412573 . A C 2758.77 . 71 58.36 INTERGENIC(MODIFIER||||||||) GT:ADSmilieP:GQ:PL 1/1:0,71:71:99:2787,214,0

chr1 602567 rs21953190 A G 5481.77 . 152 59.09 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1034|ADNP2|protein_coding|CODING|ENSCAFT00000000008|5) GT:ADSmilieP:GQ:PL 1/1:0,151:151:99:5510,430,0
Here i want to split further

Quote:
chr1 412573 . A C 2758.77 . 71 58.36 INTERGENIC(MODIFIER||||||||)
in first row into
Quote:
chr1 412573 . A C 2758.77 . 71 58.36 INTERGENIC MODIFIER
similary the data in the second row
Quote:
chr1 602567 rs21953190 A G 5481.77 . 152 59.09 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1034|ADNP2|protein_coding|CODING|ENSCAFT00000000008|5) GT:ADSmilieP:GQ:PL 1/1:0,151:151:99:5510,430,0
into
Quote:
chr1 602567 rs21953190 A G 5481.77 . 152 59.09 SYNONYMOUS_CODING LOW SILENT gaT/gaC D1034 ADNP2 protein_coding CODING ENSCAFT00000000008 5 GT:ADSmilieP:GQ:PL 1/1:0,151:151:99:5510,430,0
which means i want to replace () and | with tabs.
Last edited by mehar; 05-23-2013 at 08:52 AM..
 

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LEARN ABOUT LINUX

shtool-fixperm

SHTOOL-FIXPERM.TMP(1)					      GNU Portable Shell Tool					     SHTOOL-FIXPERM.TMP(1)

NAME

       shtool-fixperm - GNU shtool file permission fixing command

SYNOPSIS

       shtool fixperm [-v|--verbose] [-t|--trace] path [path ...]

DESCRIPTION

       shtool fixperm fixes file permissions inside a source tree under path by cleaning up the permission bits. It determines the cleaned up
       permission from the already set bits. It is intended to be run before a tarball is rolled (usually with shtool tarball) out of a source
       tree. The trick is that this is more convenient than having to set the permissions manually or by using a large file list.

OPTIONS

       The following command line options are available.

       -v, --verbose
	   Display some processing information.

       -t, --trace
	   Enable the output of the essential shell commands which are executed.

EXAMPLE

	#   Makefile.in
	dist:
	    shtool fixperm -v *
	    ...

HISTORY

       The GNU shtool fixperm command was originally written by Ralf S.  Engelschall <rse@engelschall.com> in 1996 for OSSP eperl.  It was later
       taken over into GNU shtool.

SEE ALSO

       shtool(1), chmod(1).

18-Jul-2008							   shtool 2.0.8 					     SHTOOL-FIXPERM.TMP(1)
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