use Bio::Seq;
my $seqobj = Bio::Seq->new(
    -seq => "ACTGTGTGTCC",
    -id => "Chlorella sorokiniana",
    -accession_number => "CAA41635"
);

use Data::Dumper;
Dumper($seqobj);

$seqobj->seq();

$seqobj->subseq(5,10);

$seqobj->accession_number();

$seqobj->alphabet();

$seqobj->version();

$seqobj->length();

$seqobj->desc();

$seqobj->primary_id();

$seqobj->display_id();

$trunc_seq_obj = $seqobj->trunc(5,10);

print $seqobj->seq(),"\n";
print $trunc_seq_obj->seq(),"\n";

$revcom_seq_obj=$seqobj->revcom;

print $seqobj->seq(),"\n";
print $revcom_seq_obj->seq(),"\n";

$translated_seq_obj=$seqobj->translate;

print $seqobj->seq(),"\n";
print $translated_seq_obj->seq(),"\n";

$string = "ATTGCTTT";
print $seqobj->validate_seq($string),"\n";

$string = "TTT53FFF";
print $seqobj->validate_seq($string),"\n";

$seq = $seqobj->seq();
print "$seq\n";

$length = $seqobj->length();
print "$length\n";

$subseq = $seqobj->subseq(int($length/2), $length);
print "$subseq\n";

$new_seq = $seq.$subseq;
if($seqobj->validate_seq($new_seq)){
    $seqobj->seq($new_seq);
}
print $seqobj->seq()," ", $seqobj->length(), "\n"

$translated_obj = $seq;
if( $seqobj->alphabet() == 'dna'){
    $translated_obj = $seqobj->translate();
}
print $translated_obj->seq(),"\n";

use Bio::Tools::SeqStats;
$seq_stats  =  Bio::Tools::SeqStats->new(-seq => $seqobj);

$hash_ref = $seq_stats->count_monomers();
Dumper($hash_ref);

$hash_ref = Bio::Tools::SeqStats->count_codons($seqobj);
Dumper($hash_ref);

$weight = Bio::Tools::SeqStats->get_mol_wt($seqobj);
Dumper($weight);

Bio::Tools::SeqStats->hydropathicity($seqobj);

use Bio::SeqIO;
my $seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', 
    -format => 'fasta' );

Dumper($seqio_obj );

use Bio::SeqIO;
use Bio::Seq;

my $seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', 
    -format => 'fasta' );

my $seqobj = Bio::Seq->new(
    -seq => "ACTGTGTGTCC",
    -id => "Chlorella sorokiniana"
);

$seqio_obj->write_seq($seqobj);

my $seqobj = Bio::Seq->new(
    -seq => "ACTGTGTGTCCTGTGTCC",
    -id => "Modified Chlorella sorokiniana"
);

$seqio_obj->write_seq($seqobj);

use Bio::SeqIO;

$seqio_obj = Bio::SeqIO->new(-file => "sequence.fasta", 
    -format => "fasta" );
    
while ($seq_obj = $seqio_obj->next_seq){
    print $seq_obj->seq,"\n";
}

use Bio::DB::GenBank;
$db_obj = Bio::DB::GenBank->new;

Dumper($db_obj);

use Bio::DB::GenBank;
use Bio::Seq;

$db_obj = Bio::DB::GenBank->new;
 
$seq_obj = $db_obj->get_Seq_by_id(2);

print $seq_obj->display_id(),"\n";

use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;
 
$query = "Arabidopsis[ORGN] AND topoisomerase[TITL] and 0:3000[SLEN]";
$query_obj = Bio::DB::Query::GenBank->new(-db    => 'nucleotide',  -query => $query );
 
$gb_obj = Bio::DB::GenBank->new;
 
$stream_obj = $gb_obj->get_Stream_by_query($query_obj);
 
while ($seq_obj = $stream_obj->next_seq) {     
    print $seq_obj->display_id, "\t", $seq_obj->length, "\n";
}

use Bio::SearchIO;

my $in = new Bio::SearchIO(
    -format => "blast",
    -file => "files/report.bls");
while(my $result = $in->next_result){
    while(my $hit = $result->next_hit){
        while(my $hsp = $hit->next_hsp){
            print "Query=", $result->query_name,
                " Hit=", $hit->name,
                " Length=", $hsp->length('total'),
                " Percent_id=", $hsp->percent_identity,
                "\n";
        }
    }
}