my $file=<>;

[download]
Will set $file to the first line (including the newline) read from either STDIN or the file specified on the command line. This is almost certainly not what you want.

You probably want 

my $file = shift @ARGV;  # get first argument
my $nfile = shift @ARGV; # get next argument

[download]
Which, outside of subroutines can be abbreviated to 
my $file  = shift;
my $nfile = shift;

[download]
or you can use 
my ($file,$nfile) = @ARGV;

[download]
By the way, it's always a good idea to check open() for errors: 
open FILE,">$file" or die "Can't open $file: $!"

[download]
update: there are other errors in your code, too. Note that grep() returns a LIST, for one.

"What should it profit a man, if he should win a flame war, yet lose his cool?"

In reply to Re: File read and strip by Joost
in thread File read and strip by Andrew_Levenson

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.