I wouldn't do it this way if I were you! :)

From the size it looks like you're thinking of parsing nt, which is going to be slow no matter what. The sooner you start getting used to BioPerl the better off you are. With Bio::SeqIO this is a handful of lines. Further, the tired/tireless developers there are always looking for ways to speed up their parsers. It's a real friendly mailing list, too (bioperl-l@bioperl.org).

use Bio::SeqIO;
my $seqIO = Bio::SeqIO->new({-file=>'nt', -format=>'fasta'});
my $i = 0;
while (my $seq = $seqIO->next_seq()) {
     $i++;
     }

print "There are $i non-redundant nucleotide sequences\n";
[download]

The last thing any bioinformatician wants to do is rewrite parsers. There are dozens of sequence formats, and BioPerl allows you to parse them all in this way, just changing the -format to what you need. In fact, it even has some rudimentary auto-identification, I believe. You can also rewrite sequence objects with BioSeqIO, allowing for two or three line reformatters. It's an invaluable resource, and it isn't too hard to learn to use.

BioPerl 1.2.3 is available from CPAN, or you can get a CVS tarball from the BioPerl project site.

This is a great suggestion. However, I have attempted to use the various bioperl modules, but to no avail. Again, I'm still new to computer programming in general, and the lack of good documentation for bioperl modules has left me with little more than headaches :-). I'm working on using your suggestion currently, and also intend to join the mailing list. Thanks!!
Bioinformatics

As I reread your initial post, I suspect you want to split nt into smaller chunks and write those to file. Here is a script I've been using to do that

### USAGE
# perl -w splitter.pl <filename> <seq-per-file>
# e.g. perl -w splitter.pl nt 20000

### INCLUDES
use strict;
use Bio::SeqIO;

### LOCALS
my $infile    = $ARGV[0];
my $size    = $ARGV[1];
my $i        = 0;
my $j        = 1;

### OBJECT INSTANTIATION
my $in    = Bio::SeqIO->new(
            -file    => $infile,
            -format    => 'Fasta',
            );
my $out    = Bio::SeqIO->new(
            -file    => ">$infile"."_$j.fasta",
            -format    => 'Fasta',
            );

### PROCESS FILES
while ( my $seq = $in->next_seq() ) {

    $i++;

    if ($i == $size) {
        $j++;
        $out = Bio::SeqIO->new(
                    -file    => ">$infile"."_$j.fasta",
                    -format    => 'Fasta');
        $i = 0;
        }

    $out->write_seq($seq);

    }
[download]

use strict;
use Data::Dumper;

my @seq;  # array of sequences
my %seq;  # hash lookup of sequences based on id's

{
  local $/ = '>';
  while (<DATA>) {
    s/^>//g; # strip out '>' from beginning
    s/>$//g; # and end of line
    next if !length($_);           # ignore empty lines

    my ($header_info) = /^(.*)\n/; # capture the header
    s/^(.*)\n//;                   # and strip it out

    my @rec = split /\|/, $header_info;

    s/\n//mg;                      # join the sequence strings
    push @rec, $_;                 # make sequence the last element

    push @seq, \@rec;              # push into array of sequences
        
    $seq{$rec[1]} = \@rec;         # or store in a hash lookup
  }
}

print Dumper(\@seq);
print Dumper(\%seq);

__DATA__
>gi|2695845|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobu
+lin heavy chain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGT
+ATAATAATGA
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobu
+lin heavy chain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGT
+ATAATAATGA
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
[download]

{
   local $/ = ">";
   while (<FILE>) {
      ...
   }
}
[download]

When you change that record separator to ">", that means the first record will be empty. (One of the later responses handles that case). More importantly, the last chunk of data is beyond the last record separator and there is no record separator at the End Of File (EOF). Will that last chunk be picked up at all? (I'm not exactly sure how record separators and file reads work for that last chunk.)

See perlvar $INPUT_RECORD_SEPARATOR.

#! perl -slw
use strict;
use Data::Dumper;

local $/ = '>'; # Set record delimiter

my @sequences; # AoA

(undef) = scalar <DATA>; # Discard first (blank) record.

while( my $record = <DATA> ) { # Read each paragraph

    # Split to lines
    my @lines = split "\n", $record;

    # Discard the last line if necessary
    pop @lines if $lines[-1] eq '>';

    # Build the array
    push @sequences, [ split( '\|', shift @lines), join( '', @lines ) 
+];
}

print Dumper \@sequences;

__DATA__
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobu
+lin heavychain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGT
+ATAATAATGA
CAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGAGTCCGGACCAGCAGTTATAAAGCCTGGAGA
+GTCCCATAAA
CTGTCCTGTAAAGCCTCTGGATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAA
+AGGGTCTGGA
ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGGAAGATTCGCC
+ATCTCCAGAG
ACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCTGAAGACTGAAGACACTGCCGTGTATTACTG
+TGCTCGGGGC
GGGCTGGGGTGGTCCCTTGACTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCAC
+CACCGACAGT
GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTGCTTAGCAACC
+GGATTCTGCC
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobu
+lin heavychain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGT
+ATAATAATGA
CAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGAGTCCGGACCAGCAGTTATAAAGCCTGGAGA
+GTCCCATAAA
CTGTCCTGTAAAGCCTCTGGATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAA
+AGGGTCTGGA
ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGGAAGATTCGCC
+ATCTCCAGAG
ACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCTGAAGACTGAAGACACTGCCGTGTATTACTG
+TGCTCGGGGC
GGGCTGGGGTGGTCCCTTGACTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCAC
+CACCGACAGT
GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTGCTTAGCAACC
+GGATTCTGCC
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobu
+lin heavychain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGT
+ATAATAATGA
CAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGAGTCCGGACCAGCAGTTATAAAGCCTGGAGA
+GTCCCATAAA
CTGTCCTGTAAAGCCTCTGGATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAA
+AGGGTCTGGA
ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGGAAGATTCGCC
+ATCTCCAGAG
ACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCTGAAGACTGAAGACACTGCCGTGTATTACTG
+TGCTCGGGGC
GGGCTGGGGTGGTCCCTTGACTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCAC
+CACCGACAGT
GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTGCTTAGCAACC
+GGATTCTGCC
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobu
+lin heavychain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGT
+ATAATAATGA
CAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGAGTCCGGACCAGCAGTTATAAAGCCTGGAGA
+GTCCCATAAA
CTGTCCTGTAAAGCCTCTGGATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAA
+AGGGTCTGGA
ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGGAAGATTCGCC
+ATCTCCAGAG
ACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCTGAAGACTGAAGACACTGCCGTGTATTACTG
+TGCTCGGGGC
GGGCTGGGGTGGTCCCTTGACTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCAC
+CACCGACAGT
GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTGCTTAGCAACC
+GGATTCTGCC
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
[download]

Output