[EMBOSS] CUTG

[Guy Bottu]

On Wed, Mar 10, 2004 at 09:29:16AM +0000, Peter Rice wrote:
> We are working on improving the naming and descriptions of codon usage 
> files - for EMBOSS 2.9.0. This will have to include cutgextract output.
> 
> Does anyone need the codon usage files included in the EMBOSS 
> distribution? We would like to "retire" the old ones (the long names) 
> and rename (and update) the cutg ones.

Well, there are certainly a number of things that could be done to improve 
codon usage file support in EMBOSS. I would suggest :

- let any program that handles codon usage files read in user provided
files and/or write files in several formats (as is already done for
sequences and features) : CUTG, Staden, GCG, ... 
- for the EMBOSS included files : remove redundant files (why Eeco.cut and 
Eecoli.cut ?,...), provide clear information about which is which, 
update...
 - for CUTG, let cutgextract write file names based on the ID rather then 
the species name. This would provide names that are shorter and free from 
special characters.
- still for CUTG, a system to retrieve a file over the Internet from the 
distribution site is certainly interesting, but so is a way to retrieve it 
from a local SRS (with getz).
Note by the way that CUTG has a drawback : it has a table for each 
organism without making the distinction between different gene 
populations.

	Guy Bottu,
	Belgian EMBnet Node