Remove lines from output in files using awk Post: 302976608

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Top Forums Shell Programming and Scripting Remove lines from output in files using awk Post 302976608 by RudiC on Friday 1st of July 2016 12:07:00 PM

07-01-2016

Registered User

To check for values in field 10 of any subfield identified in field 9, try

Code:

awk '
        {for (n=split ($9, TMP, ":"); n>0; n--) TYPE[TMP[n]] = n
         split ($10, VAL, ":")
         if (VAL[TYPE[SUB]] ~ PAT) next
        }
1
' SUB="GT" PAT="0/0|1/1|2/2" file
20      60056   .       G      A.       35      PASS    DP=25;PF=20;MF=5;MQ=60;SB=0.800 GT:AD:DP:GQ:FL  0/1:12,13:25:99:PASS,PASS

or, for the last subfield "FL", it yields

Code:

 SUB="FL" PAT="PASS," file
20      60055   .       A       .       35      PASS    DP=25;PF=20;MF=5;MQ=60;SB=0.800 GT:AD:DP:GQ:FL  0/0:25:25:99:PASS
20      60057   .       T       .       35      PASS    DP=26;PF=20;MF=6;MQ=60;SB=0.769 GT:AD:DP:GQ:FL  0/0:26:26:99:PASS
20      60058   .       C      T       35      PASS    DP=25;PF=20;MF=5;MQ=60;SB=0.800 GT:AD:DP:GQ:FL  1/1:25:25:99:PASS

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LEARN ABOUT CENTOS

igawk

IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME

       igawk - gawk with include files

SYNOPSIS

       igawk [ all gawk options ] -f program-file [ -- ] file ...
       igawk [ all gawk options ] [ -- ] program-text file ...

DESCRIPTION

       Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).

       AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like

	      @include getopt.awk

       in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.

OPTIONS

       See gawk(1) for a full description of the AWK language and the options that gawk supports.

EXAMPLES

       cat << EOF > test.awk
       @include getopt.awk

       BEGIN {
	    while (getopt(ARGC, ARGV, "am:q") != -1)
		 ...
       }
       EOF

       igawk -f test.awk

SEE ALSO

       gawk(1)

       Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.

AUTHOR

       Arnold Robbins (arnold@skeeve.com).

Free Software Foundation					    Nov 3 1999								  IGAWK(1)

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