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Full Discussion: awk to compare each file in two directores by storing in variable
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:
cmccabe
 

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LEARN ABOUT OPENSOLARIS

comm

comm(1) 							   User Commands							   comm(1)

NAME

       comm - select or reject lines common to two files

SYNOPSIS

       comm [-123] file1 file2

DESCRIPTION

       The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output:
       lines only in file1; lines only in file2; and lines in both files.

       If the input files were ordered according to the collating sequence of the current locale, the lines  written  will  be	in  the  collating
       sequence of the original lines. If not, the results are unspecified.

OPTIONS

       The following options are supported:

       -1    Suppresses the output column of lines unique to file1.

       -2    Suppresses the output column of lines unique to file2.

       -3    Suppresses the output column of lines duplicated in file1 and file2.

OPERANDS

       The following operands are supported:

       file1	A path name of the first file to be compared. If file1 is -, the standard input is used.

       file2	A path name of the second file to be compared. If file2 is -, the standard input is used.

USAGE

       See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes).

EXAMPLES

       Example 1 Printing a list of utilities specified by files

       If file1, file2, and file3 each contain a sorted list of utilities, the command

	 example% comm -23 file1 file2	| comm -23 - file3

       prints a list of utilities in file1 not specified by either of the other files. The entry:

	 example% comm -12 file1 file2 | comm -12 - file3

       prints a list of utilities specified by all three files. And the entry:

	 example% comm -12  file2 file3 | comm -23 -file1

       prints a list of utilities specified by both file2 and file3, but not specified in file1.

ENVIRONMENT VARIABLES

       See  environ(5)	for  descriptions  of  the  following  environment  variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE,
       LC_CTYPE, LC_MESSAGES, and NLSPATH.

EXIT STATUS

       The following exit values are returned:

       0     All input files were successfully output as specified.

       >0    An error occurred.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWesu			   |
       +-----------------------------+-----------------------------+
       |CSI			     |enabled			   |
       +-----------------------------+-----------------------------+
       |Interface Stability	     |Standard			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5)

SunOS 5.11							    3 Mar 2004								   comm(1)
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