GFF question

[David Martin]

On Thu, 17 Aug 2000, Gary Williams, Tel 01223 494522 wrote:

> David Martin wrote:
> > 
> > On Thu, 17 Aug 2000 gwilliam at hgmp.mrc.ac.uk wrote:
> > 
> > > I have two sequence that are being compared.
> > >
> > > Is it better to write out a single GFF file with the results for both
> > > sequences in it, or should I write out two separate gff files?
> > 
> > Give the user the option.
> > 
> > I can think of arguements both ways.
> 
> What are your arguments?

-ofsingle ?

but seriously, in some cases one would be wanting a GFF containing
features from many subsequences, for example if (as in our case) we are
analysing a genome containing many unordered, unconnected contigs bu twant
information such as repeat regions, ISs etc. to be kept in one place. In
other cases one may want to analyse a set of sequences but produce a
seperate file for each one, eg if one is analysin ga set of related genes
but do not want the GFF's combined.

The overall argument is that EMBOSS should be flexible an dempowering, not
conforming to any preconceived mindset (except of course that it should be
flexible and empowering, not conforming to any preconceived mindset (
except ...))

..d

> 
> Gary
> 
> -- 
> Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
> mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
> Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK
> 
> 
> 

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