This code should work but you will need to install BioPerl module Bio::SeqIO. 
use Bio::SeqIO;

# Setting minimum length to 250
my $min_len = 250;

# Reading the input fasta file
my $seqio_in = Bio::SeqIO->new(-file => "Genes.fasta", 
                             -format => "fasta" );

# Creating the output fasta file                             
my $seqio_out = Bio::SeqIO->new(-file => ">Genes_filt_250.fasta", 
                             -format => "fasta" );

# Saving sequences to the output if length > min_len     
while ( my $seq = $seqio_in->next_seq ) {
    if ( $seq->length  >  $min_len ) {
        $seqio_out->write_seq($seq);
    }
}

[download]
The sequences with length higher than 250 should be saved in file "Genes_filt_250.fasta": 
>NM_030643.4 Homo sapiens apolipoprotein L4 (APOL4) 
GAGGTGCTGGGGAGCAGCGTGTTTGCTGTGCTTGATTGTGAGCTGCTGGGAAGTTGTGAC
TTTCATTTTACCTTTCGAATTCCTGGGTATATCTTGGGGGCTGGAGGACGTGTCTGGTTA
TTATATAGGTGCACAGCTGGAGGTGAGATCCACACAGCTCAGACCAGCTGGATCTTGCTC
AGTCTCTGTCAGAGGAAGATCCCTTGGAGGAGGCCCCGCAGCGACATGGAGGGAGCTGCT
TTGCTGAAAATCTTTGTCGTCTGCATCTGGAACCAAAATC
>AC067940.1 Homo sapiens clone RP11-818E9, LOW-PASS SEQUENCE SAMPLING
AAATACAACTTTAAATCAAAACGGTAAAAATTCCACTCTTTCATACTAACTTCAAAAGTA
TTTGCTTTAAAAAAAAAGNNNNNNNNNNAAACTGAATTTCTATTAAGCATCTATTTATAG
AAGAGAGTAAACACCCCGTGAATAAAAGACAGAGAATTGTAGCAGCCCGAAGTCCCTTTT
CTCTCCTCCCAAGCATTTGGCTCTGGTCCAAATTCACATATCCTGCTCCGTAAAACAAAG
TGCCTTGGTTAACCTAACGTTATTCCTTGAACAGTAGTTTAGTGATCAACTAGTTTTTGT
TGTTGTTGTTGTTTGAGACAGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAGTGGCGAG
ATCTCAGCTCACTGCAACCTCTGCTGCCCAGGTTCAAGGGATTCTCCTGCCTCAGCCTCC
CAAGTAGCTGGTATTACAGGCACCTGCCACCGCGCCTGGCTAATTTTTTTTTTTTTTTTT
TTTTGTATTT

[download]

In reply to Re^5: Size of sequences in fastafile by zubenel0
in thread Size of sequences in fastafile by Sofie

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