[Bioperl-l] Build new Seq in SwissProt

[Marc Logghe]

Hi,
The object you created is a Bio::Seq object.
Such object can not deal with dates. You should create a Bio::Seq::RichSeq object instead.
There the add_date() method is available.Or you can pass the dates directly to the new() method (-dates => [$date1,$date]) Have a look at the Bio::Seq::RichSeq docs.
HTH,
Marc 

> -----Original Message-----
> From: hafiz hafiz [mailto:khufaz83 at yahoo.com]
> Sent: Saturday, September 18, 2004 12:04 PM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] Build new Seq in SwissProt
> 
> 
> 
> hello, help me, which bioperl modul should we use to
> insert Date  in swiss prot?
> 
> example;
> 
> ID   GRAA_HUMAN     STANDARD;      PRT;   262 AA.
> AC   P12544;
> 
> this date i mean
> DT   01-OCT-1989 (Rel. 12, Created)
> DT   01-OCT-1989 (Rel. 12, Last sequence update)
> DT   28-FEB-2003 (Rel. 41, Last annotation update)
> 
> my soure code; any suggestion
> 
> my $feat = new Bio::SeqFeature::Generic(-start
> =>10,-end => 22, -strand =>1,-primary =>"DOMAIN");
> 
> 
> 
>     
> #my @arr = $feat->get_all_tags;
> #for my $tag (@arr){
> #       print $tag,":",$feat->get_tag_values($tag),"
> ";
> #} 
>     
>                                  
> my $seq_obj =Bio::Seq
> ->new(-seq=>"attcccccchkhkhkhaaaaaaaa",-display_id
> =>"BIO52",-accession_number =>
> 'X78121',-alphabet => 'dna',-is_circular => 1);
>                                             
> $seq_obj->add_SeqFeature($feat);
> 
>     
> my $comment =Bio::Annotation::Comment->new;
> $comment->text("this looks like a good TATA box");
> my $coll =new Bio::Annotation::Collection;
> $coll->add_Annotation('comment',$comment);
> $seq_obj->annotation($coll);
>     
> $species = Bio::Species->new(-classification =>
> [@classification]);
>            # Can also pass classification
>            # array to new as below
>  $species->classification(qw( sapiens Homo Hominidae
>                                  Catarrhini Primates
> Eutheria
>                                  Mammalia Vertebrata
> Chordata
>                                  Metazoa Eukaryota ));
>                                             
>     $genus = $species->genus();
> 
>     $bi = $species->binomial();     # $bi is now "Homo
> sapiens"
> 
>     # For storing common name
>     $species->common_name("human");
> 
>     # For storing subspecies
>     $species->sub_species("accountant");
>      $seq_obj->species($species);
> my $reg = Bio::Annotation::Reference->new(  -title
> =>"SwissProt Data",
>                                             -location
> => "Gerik" ,
>                                             -authors
> =>"Muhammad hafiz Mohamed Yusof",
>                                             -medline
> => "998122",-comment=>"sdasd",-position=>"sdsadd" );
> 
>     
> 
> $seq_obj->annotation->add_Annotation('reference',
> $reg);
>     
> 
> $link2 = new Bio::Annotation::DBLink();
>    $link2->database('dbSNP');
>    $link2->primary_id('2367');   
>                                     
>    # DBLink is-a Bio::AnnotationI object, can be added
> to annotation
>    # collections, e.g. the one on features or seqs
>    $seq_obj->annotation->add_Annotation('dblink',
> $link2);
>                                  
> 
>                                             
> $file3="/home/database/Bioperl/test.gb";
>                                             
> my $io= Bio::SeqIO ->new(-format =>"swiss",-file =>
> ">$file3");
>     
> $io ->write_seq($seq_obj);
> 
> 
> 
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