[Bioperl-l] extract_feature_seq

[Charles Hauser]

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,