#11 Feature requests to generalize the approach

[Josh L. Espinoza]

Hi @yuwwu,
Thanks for creating such a great tool that has revolutionized metagenomics. I hope you are still developing this tool and plan to come out with updated versions in the future.

If so, I have 2 feature requests that can allow for much more versatility:

1. A custom protein file with a table that says "protein_X" goes to "contig_A". This could be in the form of -proteins and -protein_to_contig arguments. The reason why this will be useful is because users can use their gene modeler of choice (e.g. prodigal, transdecoder) and it could also be leveraged for protists. Which brings me to my second recommendation...
2. A custom HMM set for single copy genes such as Protist_83 from Delmont, http://merenlab.org/delmont-euk-scgs . This in combination with the above gene calls would allow researchers to leverage your tools for protists (and also remove the required dependency on fraggenescan and make it optional). This would also let users use the CPR marker set if they were looking specifically for Candidate Phyla Radiation.

Thanks,
-Josh L. Espinoza