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Top Forums Shell Programming and Scripting awk to compare each file in two directores by storing in variable Post 302982609 by RavinderSingh13 on Friday 30th of September 2016 03:08:59 PM
Old 09-30-2016
Hello cmccabe,

Could you please try to keep those both variables values into a single Input_file like as follows.
Code:
cat Input_file
S1234_ref.txt S1234_panel.vcf
A5678_ref.txt A5678_panel.vcf
T1111_ref.txt T1111_panel.vcf

Also to get the above Input_file you could use paste var_file ref_file > Input_file
Then you could try to read their values by a loop and try to put your awkinside it.
Code:
while read file1 file2
      awk '{your_logic}' $file1  $file2
done < "Input_file"

Could you please try it out and let us know how it goes then. If you have more requirements in here, kindly post with full details on same.

Thanks,
R. Singh

Last edited by RavinderSingh13; 09-30-2016 at 04:47 PM..
This User Gave Thanks to RavinderSingh13 For This Post:
 

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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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