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.

In reply to Re: simple but stuck by demerphq
in thread Base sequence length in fasta format file by lolly

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