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

[Francis Ouellette]

On 12 Apr 2000, Keith James wrote:

> Any objections (philosophical or practical)?

a philosophical one (and comment applies to GB or EMBL, or any format 
for that matter):

I think it is the begining of a very slippery and dangerous slope to
start agreeing to change a format that 1) is not controled by you 2)
is a standard for many others who expect certain format to work with
their tools.

An alternative way of thinking about the "let's not make this
ID line mandatory" model, could be to have user-controled severity
failure levels, e.g. "standard" bioperl would have maximum error level
if critical fields are missing, such as ID, AC, DE, or OS.  But one
could see a system where the bioperl users could set that to a
different level which would not result in a 'fatal error' (game over),
but maybe a 'warning' (beware of results) or an 'info' (everything is
cool) messages. This ould be explicitly noted, and users would know
why.

just my CAN$0.02, and perls of wisdom from having worked on GenBank
flat file format for many years!

cheers from the HUGO2000 meeting,

f.

--
| B.F. Francis Ouellette                      Tel: (604) 875-3815 | 
| Director, Bioinformatics Core Facility      Fax: (425) 740-6978 | 
| CMMT, UBC, Canada                        http://www.cmmt.ubc.ca | 
| francis@cmmt.ubc.ca                http://www.bioinformatics.ca |




> Date: 12 Apr 2000 13:40:36 +0100
> From: Keith James <kdj@sanger.ac.uk>
> To: vsns-bcd-perl@lists.uni-bielefeld.de
> Subject: Bioperl: EMBL format without ID/AC/DE/OS
> 
> 
> 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).
> 
> 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
> 
> 


--
| B.F. Francis Ouellette                      Tel: (604) 875-3815 | 
| Director, Bioinformatics Core Facility      Fax: (425) 740-6978 | 
| CMMT, UBC, Canada                        http://www.cmmt.ubc.ca | 
| francis@cmmt.ubc.ca                http://www.bioinformatics.ca |



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