However, there's a more convenient way, if you're up to it. In your OP, you have the command line:

perl short_path.pl input_fie output_file
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but the input and output filenames are never used in the script. To make use of them, you would access @ARGV, either explicitly or implicitly, instead of asking for the input filename.

To do so, you delete this:

print "Enter file name:\n";
chomp(my $file = <STDIN>);
open(DATA,$file) or die "failed opening file!!";
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Where you have:

ins split /,\s*/ for <DATA>;
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replace it with this (based on Athenasius's edit):

for (<>) {
    chomp;
    ins split /,\s*/;
}
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The <> is Perl DWIMmery for the magic <ARGV> filehandle, which steps through all the values in @ARGV as filenames to read from, and does the open for you. (If you expect to feed the script a list of files, you may want to add some user-friendly error checking.)

Then to execute the script:

perl short_path.pl input_file > output_file
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QM’s approach is probably the best way to go. But, for completeness: another option is to use tee from the command line. The tee command allows standard output to go to the terminal as usual, while also copying it to one or more files:

perl program.pl | tee -a output.txt
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Notes:

• The -a option appends to the file instead of overwriting it.
• You will also need to add the line:

  $| = 1;
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  or its equivalent near the top of the Perl script to force a flush after every print statement (otherwise, you won’t see the Enter file name: prompt).
• tee is standard on Unix-based operating systems. If you’re on Windows, you can download it as part of the GnuWin CoreUtils package from SourceForge.

Hope that helps,