Comments (11)
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
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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.
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Thanks Jacques. Great to read that it's not needed to include translation when submitting to ENA.
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Hi Jacques,
Will you still be including this fix for the tool? even if it is not required by ENA?
Thanks
Abhijit
from emblmygff3.
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.
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from emblmygff3.
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
from emblmygff3.
from emblmygff3.
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
from emblmygff3.
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
from emblmygff3.
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
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Related Issues (20)
- Confusion with the locus tag HOT 1
- Download HOT 27
- EMBL to fasta ? HOT 1
- How to add in comment or CC line HOT 1
- Webin-CLI validation failing due to duplicated feature locations in EMBLmyGFF3 flat file HOT 2
- thank you HOT 1
- ImportError Bio.Alphabet error HOT 1
- What the option "-a accesion" parameter should to be set(means:What type?) HOT 3
- TypeError: read() takes 1 positional argument but 2 were given? HOT 3
- attribute formats broken across several lines HOT 2
- Use of example data HOT 2
- Contigs are disorganised in the EMBL file HOT 10
- Warning qualifier unknown db_xref HOT 1
- Translation problem HOT 2
- Reporting the line number of the problematic input GFF3 files when parsing error is triggered HOT 2
- BioPython 1.81 installs via conda, but needs an older version HOT 2
- if I can specify certain python source during python setup.py install HOT 2
- Not for ENA submission: Sequence too short
- Installation issue EMBLmyGFF3 & python version requirements
- Translation when circular genome and ORF in the cut of the assembly HOT 1
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