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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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Pathway Tools compatible genbank file #203

Open kebow opened 1 year ago

kebow commented 1 year ago

Just wondering if it's possible to generate a genbank file that contains the product name from the annotations file for integration with Pathway Tools? Or maybe someone knows of a tool like emapper2gbk https://github.com/AuReMe/emapper2gbk that works with DRAM output?

rmFlynn commented 1 year ago

I think this would be great, but we don't have bandwidth at now. If you would like to make the tool, it would not be that difficult in python or R to make a basic tool, and we would give you full credit. I don't think that we have anything like this now. I think that emapper2gbk is also a good example of what it should be, mostly an independent tool that can take in maybe only the gff file and the annotations tsv file. I will leave this open in case someone can work on it some day.

dmitrisvetlov commented 1 year ago

Hello @kebow,

Could you please provide more specifics about what you are seeking that is different or additional to what DRAM currently outputs from the annotation step? In particular, what do you mean by the "product name"? The development team is trying to decide if and how we might implement this, whether in DRAM or in the upcoming DRAM 2.

Thanks, Dmitri Svetlov