gtonkinhill/panaroo

Gene coding table

Closed this issue · 4 comments

mweberr commented

Panaroo is a great approach and I am looking forward to use it. At the moment it is lacking a parameter to set the gene coding table to 11 or 4, depending on the organism studied. Otherwise I run into the following error:

 File "/lib/python3.6/site-packages/panaroo/prokka.py", line 161, in translate_sequences
    raise ValueError("Premature stop codon in a gene!")
ValueError: Premature stop codon in a gene!
gtonkinhill commented

Hi,

This is a good point. We will try and get this done for the next release.

  • 👀1
phiweger commented

Is this still an issue @gtonkinhill ?

hoelzer commented

@gtonkinhill I would be also interested in using other gene code tables as it is also already implemented for prokka! Thanks!

gtonkinhill commented

Hi all,

Sorry for the wait — I've finally got around to tackling this. I've added a new option to change the codon table to any of those offered in BioPython's generic tables.

The table can be specified using the new --codon-table parameter. At the moment it is currently only on the devel branch until I've done a bit more testing but you should be able to install this version using the following command.

pip install git+https://github.com/gtonkinhill/panaroo.git@devel