[Bioperl-l] Bio::SeqIO::embl probelms reading swissprot

Hilmar Lapp lapp@gnf.org
Mon, 11 Dec 2000 18:37:16 -0800

Murad Nayal wrote:
> -is Bio::SeqIO::embl 'supposed' to be able to read swissprot? or is
> there another implementation of SeqIO to do that (which I couldn't find
> in the 0.6.2 distribution).

SeqIO::embl is supposed to parse EMBL nucleotide entries. Swissprot is
parsed by SeqIO::swiss. Normally you shouldn't have to worry because the
right parser is instantiated automatically by Bio::SeqIO->new(), based on
what you specify for -format (Bio::SeqIO->new('-file' => "myswissprot.dat",
'-format' => "swiss") would return an Bio::SeqIO compatible stream of seq
objects, which is actually a Bio::SeqIO::swiss object). Have you tried to
instantiate Bio::SeqIO::* classes directly, and if so, why?

> -Have these bugs been reported/fixed already in the 0.7 distribution.

As I mentioned, it is not a bug. The swissprot parser as of 0.6.2 has
swissprot *writing* discouraged though, due to bugs. These are fixed in the
development trunk, hence also in 0.7.

> -when will 0.7 be available? (is read access to CVS available now to
> everyone?).

Anonymous CVS access is available, see the website (somewhere under
http://www.bioperl.org). However, due to the present 0.7-related code
transitions I discourage taking the current codebase for anything serious
unless you know what you're taking. It may stabilize again in 2-3 weeks.
0.7 is due by the end of January at the latest.

> PS: I should mention that I am encountering these problems when
> accessing the .dat file via an Index!

I have no idea what effect this may have. What is the particular way you're
accessing the file?


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