[EMBOSS] Embossdata -reject option - Checked by AntiVir DEMO versio
gbottu at ben.vub.ac.be
Wed Apr 12 09:30:00 EDT 2006
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"
values: "None, AAINDEX, CVS, CODONS, PRINTS, PROSITE, REBASE"
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
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 :
Hope this helps,
Belgian EMBnet Node
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