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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
