[Bioperl-l] extract_feature_seq

[Charles Hauser]

Got it:

my $gb = new Bio::DB::GenBank;

my $s = $f->spliced_seq($gb);


this works,

Charles

On Wed, 2004-03-24 at 10:41, Charles Hauser wrote:
> Hi,
> 
> I have cases where an mRNA (genbank) is defined by a join involving
> accessions other than the current record (see below).  
> 
> The script extract_feature_seq.PLS 
> 
> 
>     while( my $seq = $seqio->next_seq ) {    
> 	foreach my $f ( grep { $_->primary_tag =~ /$featuretype/i } 
> 			$seq->get_SeqFeatures ) {
> 	    my $s = $f->spliced_seq;
> 	    ..snip
> 	}
>    }
> 
> 
> I'm not clear how to call Bio::DB::GenBank to retrieve these accessions
> to complete the join.
> 
>     my $gb = new Bio::DB::GenBank();
>     my $seqio = $gb->get_Stream_by_acc(\@accn); 
> 
> Charles
> 
> 
> 
>      mRNA            join(<908..1024,1091..1150,1244..1447,1800..2066,
>                      2288..2888,3143..3279,3432..3601,3728..3860,4004..4243,
>                      4417..4573,4748..4923,5393..5538,5824..5989,6202..6375,
>                      AJ242524.1:1..219,AJ242525.1:136..235,AJ242525.1:357..421,
> 
> 
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