Re: Running a script across multiple directories with multiple output files (problems comparing hash key values)

I may have went in a wrong direction above.

  my %input1 = (); #initialize input1 hash
  for my $c (0..$#AbsFiles){
        if ($AbsFiles[$c] =~ /R2_001\.fastq$/){
           open INPUT1 ... ; 
           stuff to set ... $input1{$key1} ... 
           close INPUT1; 
           }
        } # c 
  for my $c (0..$#AbsFiles){
        if ($AbsFiles[$c] =~ /R1_001\.fastq$/$/){
           open INPUT2 ... ; 
           ...stuff to test key2 against $input1{$key2}; 
           close INPUT2; 
           }
        } # c
[download]

You were resetting the input1 hash every time you opened a file to test for key1.

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