I guess your main problem is that you're not reading the INPUT file mentioned in $ARGV[0]. You're reading from STDIN.

Update: davorg is correct. Anyway, s/he's not reading the file s/he thinks s/he reads.

Actually he's not reading from STDIN. He's reading from the first file named on the command line.

--
<http://www.dave.org.uk>

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg

Your problem is the line

while (<>)
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This is wrong for two reasons.

1. You've gone to the trouble of opening a specific input filehandle, INPUT, so you should be reading from that.
2. When you use the diamond operator, the first thing it does is to use shift to remove the first element from @ARGV. This means that there are now only two elements left in @ARGV and $ARGV[2] is undefined.

You should use

while (<INPUT>)
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instead.

Look for the section on "I/O Operators" in perldoc perlop.

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg

#!/usr/local/bin/perl -w
use strict;

my $params=@ARGV;
my ($input,$output,$length);

if($params < 3){
  die "Not enough parameters";
}else{
  ($input,$output,$length)= @ARGV;
}

open(INFILE,"$input")||die "Can't open $input: $!\n";
open(OUTFILE,">$output")||die "Can't open $output: $!\n";

my $count=1;

while(<INFILE>){
  chomp;
  if(/>/){ ++$count; }
  if(length($_) >= $length){
    print "\>$count\n",$line,"\n\n";
    print OUTFILE "\>$count\n",$line,"\n\n";
  }
}

close INFILE;
close OUTFILE;

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I believe this line:

($input,$output,$length)= shift @ARGV;
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should read:

($input,$output,$length)= @ARGV;
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---

Everything went worng, just as foreseen.

If it was my script, I'd write it like this:

#! /usr/local/bin/perl -w

use strict;

die "Not enough params!!!\n" if @ARGV < 3;

my ($input, $output, $length) = @ARGV;

open INPUT, $input or die "unable to open $input: $!\n";
open OUTFILE, ">$output" or die "unable to open $output: $!\n";

my $count = 1;

while (<INPUT>) {
  chomp;

  ++$count if />/;

  if (length >= $length)
    print ">$count\n$_\n\n";
    print OUTFILE ">$count\n$_\n\n";
  }
}

close INPUT;
close OUTFILE;
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--
<http://www.dave.org.uk>

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg