Most programming languages have libraries to parse Fasta (and many other sequence formats). Here's a quick example using the Bio::SeqIO library from BioPerl. It will create a new file of sequences 100 bp or less in length.

#!/usr/bin/perl -w

use strict;
use Bio::SeqIO;

my $seqin  = Bio::SeqIO->new(-file => "myfile.fa",      -format => "fasta");
my $seqout = Bio::SeqIO->new(-file => ">myfile_100.fa", -format => "fasta");
while(my $seq = $seqin->next_seq) {
  if($seq->length <= 100) {
    $seqout->write_seq($seq);
  }
}

Similar solutions exist in BioPython, BioRuby, BioJava. There are pure "non-library" solutions, but I always recommend learning how to use a Bio* library. You can also search this site for "fasta parsing" to see more advice.

Since neilfws mentioned Biopython, here is a solution using it, although this does not satisfy the OP requirements:

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import sys
from Bio import SeqIO

fasta_file = sys.argv[1]  # Input fasta file
min_length = int(sys.argv[2]) # Minimum length of sequence
result_file = sys.argv[3] # Output fasta file

fasta_sequences = SeqIO.parse(open(fasta_file),'fasta')
end = False
with open(result_file, "w") as f:
    for seq in fasta_sequences:
        if len(seq.seq.tostring()) > min_length:
            SeqIO.write([seq], f, "fasta")

Should be used as follows (after saving to script.py and making the script executable):

script.py input.fasta 100 output.fasta

Cheers

perl -ne '/length=(\d+)/; print if $1>=100' file.fa

Seems to work. Neil's BioPerl method is far more reliable though ;)

Newer BLAST version(s) have blastdbcmd which is the successor to fastacmd. You can use range option in it. It selects the range of a sequence to extract.

blastdbcmd -range "< String >"

Range of sequence to extract (Format: start-stop)

In your case 1-100

Ruby one-liner for the first option (with length in the title):

ruby -ne 'BEGIN{$/="\n>"}; length = $_.match(/length=(\d+)/)[1].to_i; print $_ if length <= 100' < in.fasta > out.fa

I have suggested one option in this thread

I have tested it by my own. It worls like gem