biopython translate error

Question

[MAK]

I want to translate a sequence which I have already parsed the translation table from the genbank file.

My code works on some of the files, but in one file I have tranlation table = 24 and I'm getting the following error:

 codon_table = CodonTable.ambiguous_generic_by_id[table_id]
KeyError: 24

The following is my code:

with open(file, 'r') as inF:
    for line in inF:
        if '/transl_table' in line:
            l=line.split('=')
            #I extracted already the gene sequence...
            protein=gene.translate(table=l[1])

What is the cause of this error and how to solve it?

[Istvan Albert]

always show the actual error that you get

[MAK]

this is the error :

codon_table = CodonTable.ambiguous_generic_by_id[table_id]
KeyError: 24

Answer 1

[Matt Shirley]

If you look at the code for CodonTable, there are only tables registered with identifiers <23. I think you'll have to either use another equivalent table (if it exists), or you can register a new one like so:

[Matt Shirley]

I've submitted a pull request to add this codon table to Biopython, so hopefully it will be in the next release.

[Matt Shirley]

Also not that I've updated the Gist to include the actual codon table you can use.