[Bioperl-l] swiss.pm again :)

Lorenz Pollak lorenz@ist.org
Tue, 1 Aug 2000 12:39:02 +0200 (CEST)

> > *) written DT Lines (Date) have no comments 
> >    (not stored in Annotation object)
> Hmmm. We could extend this object a bit, but I hate being a slave to a
> flat file format. However, the idea of different "dates" for different
> parts of the document is common-place.

the dates are stored as an arry of strings, why don't
read the whole line instead of just the date? I'll do
this in Bio::SeqIO::swiss, if you don't disagree.

Then i have another suggestion for extending the
Bio::Annotation::Comment object which for now has
only the $comment->text method:
how about $comment->special, which is undefined for
normal comments but describes the type of comment
for special comment blocks ?

> > *) Molecular Weight is different to original (?)
> Could this be the starting Met?

Could that make a difference from ca. 38000 to ca. 43000 ??

> > *) the RP line in References is not always equal, because
> >    there are $ref->start / $ref->end, which store one
> >    sequence section, but a line with multiple ones like
> >    "RP   SEQUENCE OF 1-250 AND 303-371 FROM N.A."
> >    would become
> >    "RP   SEQUENCE OF 1-250 FROM N.A."
> >    (don't know what to do about that)
> > 
> Jeez. What is going on here? Is there a swissprot guy on the list who can
> help us out here?

i have a solution for that:
$ref->start and $ref->end are stored, but also the whole
RP line in $ref->rp. and when writing we just print out

kind regards,