[Bioperl-l] swiss.pm again :)

Ewan Birney birney@ebi.ac.uk
Tue, 1 Aug 2000 09:12:38 +0100 (GMT)

On Tue, 1 Aug 2000, L.Pollak wrote:

> hi to everyone!
> i'd say, Bio::SeqIO::swiss is getting better ;)


> added suggestions from Andrew Su, who switched the
> some Reference lines and the crc code from James Gilbert!
> So now the only differences between a read swissprot and
> a written swissprot are:
> *) 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.

> *) Molecular Weight is different to original (?)

Could this be the starting Met?

> *) Line Breaks in entries that have more than one line
>    are for some reason a bit different

This is the formatting system in the dumper, and should be fine. If people
get snotty about this level of ASCII layout then I have little sympathy
for them

> *) 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?

> kind regards,
> Lorenz
> PS: test fails at SeqFeatureProducer which has no Blast.pm in
> SeqFeatureProducer subdirectory...
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420