[Bioperl-l] Bio::SeqIO::embl problems reading swissprot clarification

Hilmar Lapp lapp@gnf.org
Mon, 11 Dec 2000 19:13:15 -0800

Murad Nayal wrote:
> It seems that I was a bit too quick to post. looking more carefully now
> I see my previous message was somewhat inaccurate (sorry about that, i
> am just starting to get familiar with bioperl).
> to clarify:
> -I used Bio::Index::EMBL to index a swissprot file and subsequently
> retrieve sequences from it by id. the documentation for this class
> specifies that it can be used to index both embl and swissprot files.
> There is no Bio::Index::Swiss class.
> -the problem i encountered arouse when I tried to retrieve sequences
> using a Bio::Index::EMBL object from the previously indexed file. This
> object uses a Bio::SeqIO::embl object to read into the sequence file.
> this fails with multiple errors/warnings.
> Apparently the thing to do is to write a Bio::Index::Swiss class (which
> really can be highly similar to Bio::Index::EMBL. as far as I can see a
> subclass of Bio::Index::EMBL that overrides EMBL::_file_format() to get
> it to return "swiss" might be sufficient? this should lead to the usage
> of Bio::SeqIO::swiss instead for input (no need to modify
> Bio::SeqIO::embl).
> -Has something like that been done in 0.7?

Not yet. As what you're describing sounds like a bug, could you file a bug
report through the web-interface, copying your email as message body?

Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757