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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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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [-an] [-e s] [-o list] [-tc] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -o list Each output line comprises the fields specified in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1). BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. 7th Edition April 29, 1985 JOIN(1)
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