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);
}
}
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
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