[Bioperl-l] Features in SeqIO GenBank output

[Chris Fields]

I'll give it a look.  You might try upgrading to Bioperl 1.5.1 to see  
if this was fixed.

Chris

On Jul 20, 2006, at 5:53 AM, Georg Otto wrote:

>
> 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
> //
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign