Warning regarding protein ID

[nbisweden]

Warning regarding protein ID

[Juke34]

A new parameter could be implemented to force to accept a Qualifier value even if it doesn't respect the specification. I'm not sure to add that. Maybe in a future release.

You can easily fix that yourself:

Uninstall EMBLmyGFF3:

pip unistall EMBLmyGFF3

clone the repo in a nice place:

mkdir ~/git
cd ~/git
git clone https://github.com/NBISweden/EMBLmyGFF3.git
cd EMBLmyGFF3

Comment line 460 of the feature.py file and save the change (here using the nano text editor but you can use what ever you want):
nano EMBLmyGFF3/modules/feature.py

install:

python setup.py install

or if you do not have administartive rights on your machine:

python setup.py install --user

[Juke34]

The warning remains with this modification, but you should have the protein_id qualifier in the output now.
If it is not the case you sould also comment line 443, and un-indent line 444.

[Juke34]

e.g https://www.ebi.ac.uk/ena/WebFeat/ (=>CDS)
here the officical recommendation for the protein_id:

Qualifier	protein_id
Definition	protein identifier, issued by International collaborators. this qualifier consists of a stable ID portion (accessioned data before the end of 2018 uses a 3+5 format; from the end of 2018 new accessions may be extended to a 3+7 accession format with 3 position letters and 7 numbers) plus a version number after the decimal point.
Value Format
Example	/protein_id="AAA12345.1" /protein_id="AAA1234567.1"
Comment	when the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.

Accordingly -PB is the problem

[VenithaB]

Dear Jacques,

I checked the EMBL file available for a previous assembly provided by Ensembl (available at ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/embl/aedes_aegypti/). The file contains protein IDs of the same format as in my GFF3 file.

FT CDS 132625..133230
FT /gene="AAEL000117"
FT /protein_id="AAEL000117-PA"
FT /note="transcript_id=AAEL000117-RA"
FT /db_xref="RefSeq_peptide:XP_001657650.1"
FT /db_xref="RefSeq_dna:XM_001657600.1"
FT /db_xref="Uniprot/SPTREMBL:Q17Q75"
FT /db_xref="protein_id:EAT48841.1"
FT [/db_xref="UniParc:UPI0000DA8512"]

Is there anyway to suppress/override the above warning? I am anyway looking to only transfer annotations using RATT, not sumbit to EMBL.

[VenithaB]

Dear Jacques,

I followed your instructions and commented out the return statement in feature.py (the 460th line). I'm still getting the same warning.

[VenithaB]

It works fine, thank you.

I have one more question.

11:09:16 WARNING qualifier: Unknown db_xref 'RefSeq' - skipped.

I have references to external databases that are not supported by INSDC (http://www.insdc.org/db_xref.html), eg. RefSeq, KEGG_Enzyme etc. that I would like to retain. Can I modify the legal_dbxref.json file to include the databases?

[Juke34]

Great.
Yes definitly you can do that.