Thanks @Darren, will the code look like this? and also i want the output to be printed for respective files as different files in different directory
my $dir = '/path/to/dir';
# read only pd files:
opendir DIR, $dir or die "read dir $dir - $!";
my @pdb_files = grep /\.pdb/, readdir DIR;
foreach my $file (@pdb_files)
$output_from_my_precompiled_tool = `/path/to/my/tool $file`;
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