[Bioperl-l] Features in SeqIO GenBank output

[Georg Otto]

This indeed seems to be the case. After upgrading it works fine. Sorry
for stealing your time.

Georg


Chris Fields <cjfields at uiuc.edu> writes:

> 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