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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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passing KEGG annotations to funannotate annotate #62

Closed MichaelFokinNZ closed 7 years ago

MichaelFokinNZ commented 7 years ago

Is there any way to pass KEGG annotation to funannotate annotate, like it works for InterProScan? Actually KEGG ontology is the part of EggNog 4.5, it it possible to add them in the next revisions of funannotate?

nextgenusfs commented 7 years ago

Yes plausibly. If there is a way to add the search on the command line I can do it. I have not integrated the new eggnog mapper yet, basically right now funannotate is just doing a HMMer search using the HMM library from EggNog 4.5.

The other way in which you can always add any annotation you want is to generated an annotation file for GAG which is a 3 column tsv file that has:

mRNA-ID    note    Whatever annotation here

Have a look at the files that start with annotations.* in the annotate_misc folder. You could parse any output that you want and put it into that format and will get incorporated.

MichaelFokinNZ commented 7 years ago

Thank you! Is it just a good practice of keeping all product's names in gbf file as "hypothetical protein" , not transferring swissprot or busco annotations to the product attribute?