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

Keith James
12 Apr 2000 16:03:12 +0100

>>>>> "Francis" == Francis Ouellette <> 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 James  --  --
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA
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