[Bioperl-l] SeqIO::swiss.pm

[Ewan Birney]

On Thu, 14 Sep 2000, Hilmar Lapp wrote:

> Even though the swissprot parser has improved a lot thanks to Lorenz and
> others (maybe even myself ;) there are still some flaws in output, among
> them being e.g.
> 
> 1) superfluous empty line after the seq (does this hurt according to the
> specs?)
> 2) empty GN line (again, does this hurt?)
> 3) truncation of the OS line (at least in some cases)
> 4) OC line not being written correctly (at least in some cases)
> 
> An example is accession P25222 (SwissProt) (mentioned in bug report
> #168). I can provide the entry if you need it.
> 
> Any volunteers for fixing those things? Lorenz, still enthusiastic?
> 
> The version present in the branch-06 seems to be more or less broken, at
> least with respect to output printing. The question is whether or not we
> can take over the version from main trunk. Lorenz, could you summarize
> the modules you had to fix or even add in order to get the parser work?
> 
> I'm afraid this can break the scope of a bugfix-only. If so, replace at
> least write_seq on the branch with throwing an exception? Would be fair
> to people who assume that the result is at least half-way ok (it's not).

Hmmm. Given the fact that it never realy worked (elia was young and naive
about testing then)I think either option here is fine...

> 
> 	Hilmar
> 
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
> A-1235 Vienna                                fax: +43 1 86634 727
> -----------------------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------