[Bioperl-l] swiss.pm again :)
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