Now how do I read each filename in perl?
Well, that depends on how your program is supposed to get the filenames. Is it all files from a certain directory? Use opendir and readdir. Are the filenames given through a pipe? Use <>. Are the filenames the command line arguments? Then they are found in @ARGV. Do you use command line options to communicate filenames? Use Getopt::Long (or some other Getopt:: module).
The way I have written the code, DSSPIN produces the error:
My advice is to stop using bareword file handles. That's so last millennium. Use autovivifying filehandles: 
my $filename = "....";
open my $fh, "<", $filename or die;
while (<$fh>) {
    ...
}

[download]
Autovivifying filehandles have been there since March 2000 - when 5.6.0 got released.

In reply to Re: Confused when reading Input within Perl and Shell Scripts by JavaFan
in thread Confused when reading Input within Perl and Shell Scripts by InfoSeeker

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