Bioperl: EMBL format without ID/AC/DE/OS

[Ewan Birney]

On Thu, 13 Apr 2000, Matthew Pocock wrote:

> Hi.
> 
> One way to do this would be to parse in a ParseErrorHandler object when
> creating the parser (or the tied file handle, or whatever it is now). The
> parser would check in a paranoid manner everything that may be incorrect,
> and then inform the ParseErrorHandler. The handler would then choose to
> correct the problem, throw a warning, throw an exception, or add something
> to a log, or whatever. Two implementations of ParseErrorHandler could be
> bundled in the distribution - a fixated exception thrower, and one that is
> constructed with a user-supplied code-block that will choose what to do. If
> the no-args constructor for the parser defaults to using the paranoid
> implementation, then existing code will run unaltered.
> 
> Does this sound workable?


It does actually, but I bet you left keith behind as to what precisely to
do in terms of the perl to write. I'll chat to keith next week about how
to do this...

 > 
> Keith James wrote:
> 
> > >>>>> "Francis" == Francis Ouellette <francis@cmmt.ubc.ca> writes:
> >
> >     Francis> On 12 Apr 2000, Keith James wrote:
> >
> >     >> Any objections (philosophical or practical)?
> >
> >     Francis> a philosophical one (and comment applies to GB or EMBL,
> >     Francis> or any format for that matter):
> >
> >     Francis> I think it is the begining of a very slippery and
> >     Francis> dangerous slope to start agreeing to change a format that
> >     Francis> 1) is not controled by you 2) is a standard for many
> >     Francis> others who expect certain format to work with their
> >     Francis> tools.
> >
> > Absolutely. I certainly wouldn't expect anyone to change their
> > expectations of what EMBL or Genbank format should be.
> >
> >     Francis> An alternative way of thinking about the "let's not make
> >     Francis> this ID line mandatory" model, could be to have
> >     Francis> user-controled severity failure levels, e.g. "standard"
> >     Francis> bioperl would have maximum error level if critical fields
> >     Francis> are missing, such as ID, AC, DE, or OS.  But one could
> >     Francis> see a system where the bioperl users could set that to a
> >     Francis> different level which would not result in a 'fatal error'
> >     Francis> (game over), but maybe a 'warning' (beware of results) or
> >     Francis> an 'info' (everything is cool) messages. This ould be
> >     Francis> explicitly noted, and users would know why.
> >
> > You expressed this better than I did. The current implementation gives
> > fatal errors by default, with no means of relaxing the standard. I
> > would like some user control over the acceptable standard along with
> > an audit of what's missing.
> >
> > Keith
> >
> > --
> >
> > Keith James  --  kdj@sanger.ac.uk  --  http://www.sanger.ac.uk/Users/kdj
> > The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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