[Bioperl-l] Build new Swiss-Prot Seq

[Brian Osborne]

Hafiz,

I'm not sure I understand. Are you seeing errors when you run your code?

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of hafiz hafiz
Sent: Thursday, September 16, 2004 8:00 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Build new Swiss-Prot Seq


Hello , everybody can help me, i want to buid a new
sequence in swissprot and i have used  3 modul such as
Bio::SeqFeature, Bio::Seq, Bio::Annotation::Comments,
Bio::Annotation::Simplevalue, Bio::Annotation
Bio::Annotation::references and
Bio::Annotation::Dblink,  so it's true or not.

This is my souces code;

$feat = new Bio::SeqFeature::Generic ( -start => 10,
-end => 100,
                                -strand => -1,
-primary => 'repeat',
                                -source_tag   =>
'repeatmasker',
                                -display_name => 'alu
family',
                                -score  => 1000,
                                -tag    => {
                                    new => 1,
                                    author =>
'someone',
                                    sillytag => 'this
is silly!' } );



#my $feat = new Bio::SeqFeature::Generic(-start
=>10,-end => 22, -strand =>1,
#                                       -tag =>{
author => 'john',note =>'TATA box'});




$feat->add_tag_value("match1","PF000123 e-7.2");
$feat->add_tag_value("match2","PF002534 e-7.2");

my @arr = $feat->get_all_tags;
for my $tag (@arr){
        print $tag,":",$feat->get_tag_values($tag),"
";
}




my $seq_obj =Bio::Seq
->new(-seq=>"attcccccchjkhjkhkjh",
-display_id=>"BIO52" );
$seq_obj->add_SeqFeature($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);

  my $col = new Bio::Annotation::Collection;
   my $sv = new Bio::Annotation::SimpleValue(-value =>
'someval');
   $col->add_Annotation('tagname', $sv);

    $reg = Bio::Annotation::Reference->new( -title =>
'title line',
                                            -location
=> 'location line',
                                            -authors
=> 'author line',
                                            -medline
=> 998122 );


 $link1 = new Bio::Annotation::DBLink(-database =>
'TSC',
                                        -primary_id =>
'TSC0000030'
                                        );

   #or

   $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

$feat->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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