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Notes on application for codon usage / composition bias

Correspondence on new application for showing codon usage tables: > 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. Yes, that makes sense now ! > 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 Yeah, that is of course the most obvious ;-) Thing is that I wanted to do it in an emboss-only way so that it would be possible to run the emboss command via a soaplab service. The latter should provide a means to dynamically fetch a list of codon usage tables. More or less like showdb is doing. > > Hope this helps, We are looking at ways to do that ... can be tricky if cutgextract has been run. Any suggestions? A showdata application perhaps? Hope that helps, Peter 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'.

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