Is your feature request related to a problem? Please describe.
I'm working on updating my VEBA metagenomics software suite (https://github.com/jolespin/veba) and working on scaling up the workflows to being able to hand thousands of samples. In this, I'm in the process of reducing redundancies. The big one for the prokaryotic binning is recomputing the gene predictions since I've already precomputed them w/ Pyrodigal. I want to add MetaCoAG to my software in the new version but I noticed that it's recomputing gene predictions.
Describe the solution you'd like
Provide 2 additional arguments:
--proteins /path/to/proteins.fasta for entire assembly
--proteins_to_contigs /path/to/tsv tabular format with column 1 being proteins and column 2 being contigs
Describe alternatives you've considered
Factoring in overhead costs of recomputing existing genes
Additional context
This feature will make the tool more flexible and easily scalable to larger projects
Is your feature request related to a problem? Please describe.
I'm working on updating my VEBA metagenomics software suite (https://github.com/jolespin/veba) and working on scaling up the workflows to being able to hand thousands of samples. In this, I'm in the process of reducing redundancies. The big one for the prokaryotic binning is recomputing the gene predictions since I've already precomputed them w/ Pyrodigal. I want to add MetaCoAG to my software in the new version but I noticed that it's recomputing gene predictions.
Describe the solution you'd like
Provide 2 additional arguments:
Describe alternatives you've considered
Factoring in overhead costs of recomputing existing genes
Additional context
This feature will make the tool more flexible and easily scalable to larger projects