Hi, hopefully you are actually indenting your work and that it got unindented by not using code tags.

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

use strict;

open (INPUT, $ARGV[0]) or die "unable to open file";
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This is precisely what the perl idiom while (<>){} is for

my $sequence;
my $count =0;
my $base = ("A"|"C"|"G"|"T");
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This probably doesnt do what you want. $base ends up being the binary or of the string A C G and T. Which happens to be "W". :-)

my @array;
my $ideal = 250;

while (<INPUT>)
{
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As i said before the while loop can be rewritten much cleaner. Also you are reading in a line at a time because you havent messed with $/

$sequence = $_;
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No need to save $_ unless intend to do something that will smash it. Which afact you arent.

@array = ();
@array = split (/\n/, $sequence);
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You read in a line, and then you split by \n. That wont help as there will only be 1 (or 0) but not more. So everything from there isnt going to go well. :-)

Maybe this does what you want, or least points you in the right direction?

while (<>) {
  chomp; # lose potential newlines at the end. (only needed for portab
+ility)
  print $_,"\n" if length $_ > 250;  # print out any sequence longer t
+han 250chars
}
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One of the cool things about the while (<>) idiom is that it will allow you to do this:

# find every line over 250 chars from three different files, print the
+m to STDOUT
over_250 file.1 file.2 file.3
# find lines over 250 chars from STDIN
over_250 <file.1
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HTH

Yves / DeMerphq
---
Writing a good benchmark isnt as easy as it might look.

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