#!/usr/bin/perl -w
use Bio::SeqIO;

use Bio::Seq;
 
$seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' );
 
print $seq_obj->seq;



$seqfile = $ARGV[0];

#simple retrieval
 
$seqio_obj = Bio::SeqIO->new(-file => $seqfile, -format => "fasta" );

$seq_obj = $seqio_obj->next_seq;

#simple write

$seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt",                        
                         -display_id => "#12345",                        
                         -desc => "example 1",                        
			 -alphabet => "dna" );
 
$seqio_obj = Bio::SeqIO->new(-file => '>out.fasta', -format => 'fasta' );
 
$seqio_obj->write_seq($seq_obj);

use Bio::DB::Fasta;

#indexing file for fast retrieval
 
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
 
$db = Bio::DB::Fasta->new($file);
 
$seqobj = $db->get_Seq_by_id($id,$start,$end);
 
print $seqobj->seq;