[Bioperl-l] Build new Seq in SwissProt
hafiz hafiz
khufaz83 at yahoo.com
Sat Sep 18 06:03:39 EDT 2004
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);
________________________________________________________________________
Yahoo! Messenger - Communicate instantly..."Ping"
your friends today! Download Messenger Now
http://uk.messenger.yahoo.com/download/index.html
More information about the Bioperl-l
mailing list