[Bioperl-l] How do you create a genbank file?

[Marc Logghe]

> You can set GI number with
> $seq->primary_id($ginumber);

True. You can set it up in the object but it is not shown in the genbank dump. And, also the way around, when a genbank record is parsed containing the line 'VERSION     AB050006.1  GI:26453358' it does not get into the Bio::Seq::RichSeq object. As far as I can see.

> 
> If you want to be creating RichSeq instead of Bio::Seq objects (in the
> event you want to set some fields which are only available in RichSeq
> objects, initialize your  Bio::SeqIO fasta parser like this:
> 
> use Bio::SeqIO;
> use Bio::Seq::SeqFactory;
> my $seqio = new Bio::SeqIO(-format => 'fasta',
> 			   -file   => $file,
> 			   -seqfactory => new Bio::Seq::SeqFactory
> 			( -type => 'Bio::Seq::RichSeq'));
That is a really cool one. Never used it like this. Thanks
ML