[Bioperl-l] Features in SeqIO GenBank output

[Georg Otto]

Hi,

this is probably a FAQ but I could not find anything to solve it.

I want to get sequences from GenBank and save them in GenBank
format. This works with the script shown below, but the "Features"
part is missing and contains references instead (see below). How can I
print out the complete GenBank entry?

I am running Bioperl 1.5, Perl 5.8.6, Mac 10.4.7

Best,

Georg



Here is my script:

use strict;
use warnings;

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


my $acc = 'AB017118';
my $db_obj = Bio::DB::GenBank->new();
my $seq_obj = $db_obj-> get_Seq_by_acc($acc);
my $out = Bio::SeqIO->new(-format => 'genbank',
			    -file => '>output.gb');
$out->write_seq($seq_obj);



Here is the output:

LOCUS       AB017118                2038 bp    mRNA    linear   VRT 06-JUN-2006
DEFINITION  Danio rerio mRNA for ornithine decarboxylase antizyme long
            isoform, complete cds.
ACCESSION   AB017118
VERSION     AB017118.1  GI:4239978
KEYWORDS    .
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Cyprinidae; Danio.
REFERENCE   1
  AUTHORS   Saito,T., Hascilowicz,T., Ohkido,I., Kikuchi,Y., Okamoto,H.,
            Hayashi,S., Murakami,Y. and Matsufuji,S.
  TITLE     Two zebrafish (Danio rerio) antizymes with different expression
            and activities
  JOURNAL   Biochem. J. 345 PT 1, 99-106 (2000)
   PUBMED   10600644
REFERENCE   2  (bases 1 to 2038)
  AUTHORS   Matsufuji,S. and Saito,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-AUG-1998) Senya Matsufuji, Jikei University School
            of Medicine, Department of Biochemistry II; 3-25-8 Nishishinbashi,
            Minato-ku, Tokyo 105-8461, Japan (E-mail:senya at jikei.ac.jp,
            Tel:+81-3-3433-1111(ex.2276), Fax:+81-3-3436-3897)
FEATURES             Location/Qualifiers
     source          1..2038
                     /db_xref="Bio::Annotation::SimpleValue=HASH(0x19b9a28)"
                     /mol_type="Bio::Annotation::SimpleValue=HASH(0x19b9b6c)"
                     /dev_stage="Bio::Annotation::SimpleValue=HASH(0x19b9bb4)"
                     /organism="Bio::Annotation::SimpleValue=HASH(0x19bfe18)"
                     /clone_lib="Bio::Annotation::SimpleValue=HASH(0x19bfe60)"
     CDS             join(45..224,226..702)
                     /db_xref="Bio::Annotation::SimpleValue=HASH(0x19c0960)"
                     /ribosomal_slippage="Bio::Annotation::SimpleValue=HASH(0x1
                     9beecc)"
                     /codon_start=Bio::Annotation::SimpleValue=HASH(0x19bef14)
                     /protein_id="Bio::Annotation::SimpleValue=HASH(0x19bef5c)"
                     /translation="Bio::Annotation::SimpleValue=HASH(0x19befa4)
                     "
                     /product="Bio::Annotation::SimpleValue=HASH(0x19befec)"
                     /note="Bio::Annotation::SimpleValue=HASH(0x19bf034)"
     CDS             45..227
                     /db_xref="Bio::Annotation::SimpleValue=HASH(0x19bee24)"
                     /codon_start=Bio::Annotation::SimpleValue=HASH(0x19bf160)
                     /protein_id="Bio::Annotation::SimpleValue=HASH(0x19bf1cc)"
                     /translation="Bio::Annotation::SimpleValue=HASH(0x19c1830)
                     "
                     /note="Bio::Annotation::SimpleValue=HASH(0x19c1878)"
     polyA_signal    2017..2022
     polyA_site      2038
                     /note="Bio::Annotation::SimpleValue=HASH(0x19bffc8)"
BASE COUNT      439 a    377 c    532 g    690 t
ORIGIN      
        1 cagcagccga gcgcacaggc cgccgtgaaa cctcccgagg ccggatggta aaatccaacc


<snip>

     1981 ttatcctcta tagtggtaca cctttgcttc tgtcataata aaaccattat ttaaagac
//