You can cycle through all the files with that pattern with glob.

Something like that (untested code):

#!/usr/bin/perl
use strict;
use warnings;

for ( glob data*R.fa ) {
    my $Rfile = $_;
    s/R(?=\.fa)$/P/;
    my $Pfile = $_;
        # Your code here
}

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In reply to Re: Finding Files and Processing them iteratively by deibyz
in thread Finding Files and Processing them iteratively by monkfan

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