[Bioperl-l] Bio::DB::Fasta + Bio::SeqIO

[Jason Stajich]

Bio::DB::Fasta returns Bio::PrimarySeq::Fasta objects which are  
perfectly fine to write with Bio::SeqIO::fasta but not for any of the  
rich-seq writers.
Do we think this is a bug or feature.  The solution is to write the  
PrimarySeq wrapped in a Bio::Seq object.

See this gist -- I would imagine this as additional test lines in t/ 
LocalDB/DBFasta.t but I don't know what we really expect?
http://gist.github.com/183169

I also notice that $seq->description & $seq->display_id don't allow  
'set' option - which probably makes sense since this is a read-only  
object that came from the DB, but it basically silently ignores set.   
I often do this if I pull seqs from a DB::Fasta db and re-format the  
IDs or description line.  So I end up making a new object and copying  
the data over.  I *think* this is really a feature not a bug, just  
wanted to bring it up.

-jason
--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org