If I'm reading what you're trying to do correctly, you're trying to read sequences from a FastA format file, count the length of each sequence, and print out the ones that are more than 250 bases long.

If possible, I'd suggest using the bioperl module. That does all of the work of reading fasta format, and so will make your work easier. If you can't install modules yourself, perhaps you can get your system administrator to install it for you.

Here's an example of what I think you're trying to do, using the BioPerl modules.

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

### NOT TESTED CODE-- I'm not a bio guy, and don't have BioPerl...

use strict;

use constant IDEAL => 250;

use Bio::SeqIO;

MAIN: {
  my $seq_file = Bio::SeqIO->new(
                                 -file => $ARGV[0],
                                 -format => 'fasta'
                                )
    or die "Couldn't open $ARGV[0]: $!; stopped";

  while ( my $seq = $seq_file->next_seq() ) {
    if ( $seq->length() > IDEAL ) {
      print $seq->seq(), "\n";
    }
  }
}
[download]

stephen

Update: Removed redundant length() call.