List of valid tables for Seq.translate()

Question

[hydrofilie]

Is there a way to get the list of valid values for table argument of the translate() method programatically?

Or, if I want to try all, do I need to provide the list of the valid tables manually?

[Matt Shirley]

Are you referring to BioPython Seq.translate() or Python string.translate()?

[hydrofilie]

Seq.translate()

Answer 1

[Matt Shirley]

Take a look at the end of this file, where the codon tables are defined.

EDIT

Looks like you just need to do:

>>> from Bio.Data.CodonTable import generic_by_name

>>> generic_by_name.keys()

dict_keys(['Hexamita Nuclear', 'SGC4', 'Alternative Yeast Nuclear', 'SGC1', 'SGC8', 'Standard', 'SGC9', 'Yeast Mitochondrial', 'Scenedesmus obliquus Mitochondrial', 'Plant Plastid', 'Alternative Flatworm Mitochondrial', 'Ascidian Mitochondrial', 'Vertebrate Mitochondrial', 'SGC0', 'Dasycladacean Nuclear', 'Coelenterate Mitochondrial', 'Invertebrate Mitochondrial', 'Trematode Mitochondrial', 'Bacterial', 'Flatworm Mitochondrial', 'Echinoderm Mitochondrial', 'Mycoplasma', 'Blepharisma Macronuclear', 'SGC2', 'Ciliate Nuclear', 'Thraustochytrium Mitochondrial', 'Mold Mitochondrial', 'Euplotid Nuclear', 'Chlorophycean Mitochondrial', 'Spiroplasma', 'SGC5', 'SGC3', 'Protozoan Mitochondrial'])

[Matt Shirley]

If I have time I'll look into adding this as a new function.

[hydrofilie]

that would be great, thanks

[hydrofilie]

I have found that already, but the problem is, that new codes may be added/removed and I want the program to know all codes in the recent version without rewriting the code after each change.

[Matt Shirley]

Take a look at my edit. It seems like you can already find this list of codes.