[Bioperl-l] Re: SeqIO::swiss.pm

[Lorenz Pollak]

> 1) superfluous empty line after the seq (does this hurt according to the
> specs?)

done.

> 2) empty GN line (again, does this hurt?)

quickfix but done. :-)

> 3) truncation of the OS line (at least in some cases)
> 4) OC line not being written correctly (at least in some cases)

ok, after having read the swissprot specs (dont know if it
had been clear to you) i discovered that viruses have some different
formats in the OS and OC lines. so what i'm doing is checking if the
kingdom is =~ /viruses/i and then reading and writing the classification 
in a slightly different way.

not very elegant, but as far as i can tell its at least working.

> An example is accession P25222 (SwissProt) (mentioned in bug report
> #168). I can provide the entry if you need it.

there's also another bug i've discovered by reading and writing
protein P25222: there is a new format in the RX line of a
literature reference! even in my swissprot specs file from
may 2000 i couldnt find anything about this.

it should be
RX   MEDLINE; 12345678.

but it is
RX   MEDLINE=90278420; PubMed=2161902;

what shall i do about this? (the Bio::Annotation::Reference Object has no
property for that PubMed Reference yet)


good night to all of you,
Lorenz