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

[Ewan Birney]

On 12 Apr 2000, Keith James wrote:

> 
> Hi,
> 
> At the moment the EMBL SeqIO module requires certain things of an EMBL
> entry. Some are quite explicit (throws exception if ID is missing),
> while others are less so (dies with Perl pattern matching error if DE
> and OS are missing).

The silent death is definitely bad. I think we have to keep somethings (eg
an ID?) otherwise it will be almost impossible to know when we are not
parsing EMBL.

Otherwise, loosening the parser is fine. I don't think that optional
things (eg, DE lines) even warrant issueing a warning.

coping with any-order of tags before the FT line might be interesting.
Have fun - make sure you are doing this on the main trunk...



 > 
> I'd like to propose that it be a bit less dictatorial about these and
> still parse the entry. By all means there should be an optional
> warning of missing fields (with the default being to issue warnings).
> 
> The reason I suggest this is purely self interest (or rather, in the
> interests of our group) as the majority of our entries contain
> analytical results which we feed to Artemis. They are always being
> cat'ed togther so non-FT fields make things very awkward.
> 
> Any objections (philosophical or practical)?
> 
> 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
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