Hi zajtat,
Yes, the first invocation of combining.executable:

Code:

./match.pl -f 9477885102_R01C02header -g 9477885102_R01C01header -k 1 -l 1 -v '5 6 7' > 0

creates a file named 0 and the second invocation of combining.executable:

Code:

./match.pl -f 9477885102_R02C01header -g 0 -k 1 -l 1 -v '5 6 7' > 1

uses file 0 and creates file 1. Subsequent passes through the loop alternate between creating file 0 and using file 1 on odd numbered invocations (after invocation 1) and creating file 1 and using file 0 on even numbered invocations.

And, on OS X, the script I suggested works with both bash (version: GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin15)) and with ksh producing the output you said you wanted with the three input files you provided as samples in post #1 in this thread (except the order of the 1st two lines in the output was switched) with combining.executable being the script:

Code:

#!/bin/bash
awk '
FNR == NR {
	k[$1, $2, $3] = $0
	next
}
($1, $2, $3) in k {
	print k[$1, $2, $3], $(NF - 2), $(NF - 1), $NF
	next
}
1' "$2" "$1"

which works fine as long as the input files are text files. Note that with the number of files you are combining, the above script might or might not work. The awk utility is only required to work on text files and some of the files this script will be processing will not be text files (due to excessive line lengths).

If your perl script won't accept 0 as a filename, that is your problem. The script I provided (after changing the 1st line to use your shell) meets all of your specifications.

If you would like to give us a clear specification of the allowed filenames for the -g option to your perl script, I might be able to help you make the script I suggested use different temporary filenames.