[EMBOSS] Embossdata -reject option

[Marc Logghe]

Hi Peter,

> Hmmmm .... yes, -help and the acdtable output (the table in 
> the webpage application documentation) really need to report 
> the list of menu items for values that are not prompted (list 
> and selection datatypes).
> 
> We will do that for the next release!
> 
> Otherwise, you do need to look in the ACD file.
> 
> I propose:
> 
> -help to report documentation on the options -help -verbose 
> to report the list of options
> 
> acdtable to report the full menu formatted in the "Allowed 
> values" box.

OK, great !

> We are looking at ways to do that ... can be tricky if 
> cutgextract has been run. Any suggestions? A showdata 
> application perhaps?

Yes that could be a start. You could give the directory name as a
parameter, the oposite of the -reject parameter (-include ?).
In it's basic form it can just list the file content like embossdata
-showall is doing.
An example command that lists all the codon tables could be: 'showdata
-include CODONS'.

Something else. In order not to contaminate the CODONS folder I created
a CUTG folder in the <emboss_data> directory containing the codon tables
extracted from the most recent CUTG. Problem now is a user has to add
the relative filename as a cfile option (backtranseq) in order EMBOSS to
find the new codon tables. Would it be an idea that you can set
$EMBOSS_DATA to a list of values instead of only 1 directory name ? In
that way, EMBOSS can access custom data directories.
Suppose the following:
EMBOSS_DATA=/usr/local/share/EMBOSS/data:/my/other/emboss_data_dir/CUTG

If a codon table is not found in the usual place
(/usr/local/share/EMBOSS/data/CODONS) EMBOSS will look for them in other
places defined in EMBOSS_DATA (/my/other/emboss_data_dir/CUTG). Or
something alike.

Does that make sense ?
Cheers,
Marc