--translate option does not work anymore

[Juke34]

line 607 of feature.py has to be replaced by
translated_seq = str(seq.translate(codon_table)).replace('B','X').replace('Z','X').replace('J','X')

[Jeepee8820]

Hi Jacques,

Sorry to bother you again but it seems to me that the translate option does not take into consideration the change to Met when at start. I used the parameters --transl_table 11 and --translate and Webin CLI complains about ERROR: Expected and conceptual translations are different. The translations at these positions do indeed start with L, I or V instead of M.
Any fix possible? Thanks in advance

[Juke34]

Right good catch! If biopython deals with that it should be fixable easily otherwise I would need to implement something. Anyway, You do not need to include the translation when submitting to ENA. They will do it for you. This option is actually not really useful for submission purpose.

[Jeepee8820]

Thanks Jacques. Great to read that it's not needed to include translation when submitting to ENA.

[sanyalab]

Hi Jacques,

Will you still be including this fix for the tool? even if it is not required by ENA?

Thanks
Abhijit

[Juke34]

It is planned, but I cannot tell you when. At the latest when I will be back from parental leave in November 😁. Otherwise everyone is welcome to PR the required changes.

[sanyalab]

Hey, Congratulations Jacques. Lovely news. Enjoy paternity leave. I'll use the 1.3 version for now. The protein translation works in that. Thanks Abhijit

…

On Wed, Jul 15, 2020 at 2:45 AM Jacques Dainat ***@***.***> wrote: It is planned, but I cannot tell you when. At the latest when I will be back from parental leave in November 😁. Otherwise everyone is welcome to PR the required changes. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE545CKINZBFNRLFFF2ARJDR3TDGJANCNFSM4N2FFJOA> .

[Juke34]

Should be fixed by now. You can try it by installing the version in the speed branch.
I will soon merge it to the master branch and then release an official new version

[sanyalab]

Ok... Thank you Jacques. I have another query w.r.t AGAT. I am using it through conda. I cannot find "agat_sq_manage_ID <https://github.com/NBISweden/AGAT/wiki/agat_sq_manage_ID>" in the release 0.5.0 on conda. If I download the script into the folder with the other AGAT scripts and the conda environment, will that work? Thanks Abhijit

…

On Wed, Oct 21, 2020 at 4:44 PM Jacques Dainat ***@***.***> wrote: Should be fixed by now. You can try it by installing the version in the speed branch. I will soon merge it to the master branch and then release an official new version — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE545CMSRDONPLM26MRMM23SL27ALANCNFSM4N2FFJOA> .

[Juke34]

Better to ask that kind of thing on the related Repo to keep the thread clear. The script is definitely in AGAT: https://github.com/NBISweden/AGAT/tree/master/bin
But the name is slightly different now agat_sq_manage_IDs.pl. The wiki is from an older version

[sanyalab]

Should be fixed by now. You can try it by installing the version in the speed branch.
I will soon merge it to the master branch and then release an official new version

Hi Jacques,

Is the above fix in Conda? I have the tool installed via anaconda.

Thanks
Abhijit

[Juke34]

Hi @sanyalab, I didn't merge the branch waiting for feeback from users.
If you want to use this branch just install over the emblymygff3 conda env you already have or create a new env follwing theses steps:

conda create -n emblmygff3_speed
conda activate emblmygff3_speed
conda --install -c bioconda emblmygff3
git clone https://github.com/NBISweden/EMBLmyGFF3.git
cd EMBLmyGFF3
git checkout speed
python setup.py install

Then you can use EMBLmyGFF3 normally