This is a test version of Biostars. For the public version, visit https://www.biostars.org.
biopython translate error

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?

biopython genbank codon translation python
• 3,218 views • link
updated by Ram Ram • written by MAK • MAK

always show the actual error that you get

• 0 views • link
written by Istvan Albert Istvan Albert

this is the error :

codon_table = CodonTable.ambiguous_generic_by_id[table_id]
KeyError: 24
• 0 views • link
updated by Ram Ram • written by MAK • MAK

1 answer

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:

• 0 views • link
updated by Ram Ram • written by Matt Shirley Matt Shirley

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

• 0 views • link
written by Matt Shirley Matt Shirley

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

• 0 views • link
written by Matt Shirley Matt Shirley

Log in to answer this question.

More posts like this