[EMBOSS] Embossdata -reject option - Checked by AntiVir DEMO versio

[Guy Bottu]

On Wed, Apr 12, 2006 at 02:39:00PM +0200, Marc Logghe wrote:
> I am intrigued by the -reject option of embossdata.
> According to the doc:
> "This specifies the names of the sub-directories of the EMBOSS data
> directory that should be ignored when displaying data directories.
> Choose from selection list of values 	3, 5, 6".
> I was not able to find out what this list of values corresponds to.

Indeed tricky to find out what this means   :-;
You can look in the file  .../share/EMBOSS/acd/embossdata.acd :

  selection: reject  [
    default: "3, 5, 6"
    minimum: "1"
    maximum: "6"
    values: "None, AAINDEX, CVS, CODONS, PRINTS, PROSITE, REBASE"
    delimiter: ","
    header: "Directories to ignore"
    information: "Select directories"
    help: "This specifies the names of the sub-directories of the
           EMBOSS data directory that should be ignored when displaying data
           directories."
    button: "Y"
  ]

So, by default CVS, PRINTS and PROSITE are rejected.

> I hoped to get a list to select from when embossdata was run with the
> -options parameter, but this did not happen.

That is because -reject is an "advanced", not an "optional"/"additinal" 
parameter. It is indeed impossible to get a selection list displayed at 
the command line, although many GUI's like wEMBOSS will show it.

> Actually I was trying to find a way to obtain more or less the oposite
> of '-reject', e.g. what if you only want the content of the CODONS
> directory ?

This does not work, there is no way to reject the files in the base data 
directory. The best you can do is to add on the command line 
-reject=2,3,5,6,7 or -reject= AAINDEX,CVS,PRINTS,PROSITE,REBASE
What you can do however is :
ls $EMBOSS_DATA/CODONS

	Hope this helps,
	Guy Bottu,
	Belgian EMBnet Node