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Full Discussion: AWK:Split fields separated by semicolon
Top Forums Shell Programming and Scripting AWK:Split fields separated by semicolon Post 302596450 by brianjb on Tuesday 7th of February 2012 12:06:37 PM
Old 02-07-2012
Kind of cumbersome I know, but the first thing we needed to do was clean up the file with sed then use awk.

The file awk.test contains the following:

Code:
1 3000012 . A G 126 . DP=51;VDB=0.0000;AF1=1;AC1=2;DP4=3,0,47,1;MQ=31;FQ=-99;PV4=1,1,0.31,1

Code:
sed -e 's: * :;:g' awk.test \
| sed 's:[A-Z][A-Z][A-Z]=::g' \
| sed -e 's:[A-Z][A-Z][A-Z][0-9]=::'g \
| sed -e 's:[A-Z][A-Z][0-9]=::g' \
| sed -e 's:[A-Z][A-Z]=::g' \
| awk -F\; '{print$1" "$2" "$3" "$4" "$5" "$6" "$7" "$8" "$9" "$10" "$11" "$12" "$13" "$14" "$15}'

The first sed command is cleaning up the white space in the beginning and replacing it with semicolon. The next 4 sed commands are getting rid of the identifier and just leaving it with the value. Once everything is done, the last awk command prints out your results.

Let me know if this helps or if you need more.


That produces this:
Code:
1 3000012 . A G 126 . 51 0.0000 1 2 3,0,47,1 31 -99 1,1,0.31,1

Last edited by Franklin52; 02-08-2012 at 06:03 AM.. Reason: Please use code tags for code and data samples, thank you
 

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VCF-COMPARE(1)							   User Commands						    VCF-COMPARE(1)

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SYNOPSIS

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DESCRIPTION

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OPTIONS

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	      per line in a file. The names are colon separated and must appear in the same order as the files on the command line.

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