any ideas on how to Print the converted values out into another tab-delimited file of equal dimensions

Just open an output file, and print to that file handle, instead of printing to (the default) STDOUT; that is:

...
open OUT, ">", "outfile.name" or die "outfile.name: $!\n";
...
print OUT $DNA_conc;
# and so on...
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Or, you could just use redirection on the shell command line, but for that to be effective, you want to use @ARGV for user input to the script, rather than printing a prompt to ask for input -- that is:

# don't do this:
#  print " Enter the number. \n";
#  chomp ($df = <STDIN>);
# do this instead:
die "Usage: $0  multiplier_value\n"
    unless ( @ARGV == 1 and $ARG[0] =~ /([\d.]+)/ );

my $df = $1;
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(The sanity check on the @ARGV value is not exactly a perfect one for checking that a string is a valid numeric -- e.g. it won't accept negative numbers -- but it's more than what you've been doing so far, and every little bit helps.)

Doing it that way, your shell command line would go like this, to set the value (e.g. to "10.5") and redirect output to some other file:

    your_script_name 10.5 > outfile.name
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As a rule, it makes sense to use @ARGV for the input file name too -- in fact, perl defaults to reading file names given as command-line args. I would do your script like this:

#!/usr/bin/perl

use strict;
use Regexp::Common;

die "Usage: $0 multiplier_number [input.file]\n"
    unless ( @ARGV and $ARGV[0] =~ /^$RE{num}{real}$/ );

my $df = shift;  # take the numeric arg off @ARGV

while (<>)   # read from STDIN, or from file(s) named in @ARGV
{
    if ( ! /^\s*(?:$RE{num}{real}\s+)+$/ ) {   # if line has non-numer
+ics
        print;
    }
    else {
        my @vals = map { $_ * $df * 50 } split;
        print join( "\t", @vals ), "\n";
    }
}
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That also uses a better method of checking for numbers. Run it like this:

 script_name  10  input.txt > 10_x_50_x_input.txt
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