generate multiple output types and/or reuse intermediate files

[arkadiy-garber]

generate multiple output types and/or reuse intermediate files

[Arkadiy-Garber]

Hi,

Thanks for this comment, that sounds like a great idea! If you provide FeGenie with an output directory (using -out flag) that already exists, FeGenie will look into that directory and attempt to find corresponding ORF calls for each provided FASTA file. This should get around the time-consuming step of ORF prediction in large metagenomes. I need to make this feature of FeGenie clear in the Wiki/README.

As far as skipping HMM searching, that is not something that was an option for FeGenie. But I just enabled a new flag (--skip). If you provide this flag, along with all the other flags that you provided in a previous run (-bin_dir, -bin_ext, -out, etc.), FeGenie should skip all the time-consuming steps (including ORF prediction and HMM searching) and move directly to creating the "FeGenie-heatmap-data.csv" file that features the various flavors of output. Let me know if you have any questions or issues getting that flag to work.

Thanks again for using FeGenie! Hope you find it useful to your research.

Thanks,
Arkadiy

[gabriellerocap]

Thank you! I tried out the --skip function successfully. lt did overwrite my previous FeGenie-heatmap-data.csv file, but as long as that is clear in the readme so the user has a headsup to rename the first one, I think it is fine. It is so much faster!

[Arkadiy-Garber]

Thanks for letting me know! I will make that clear in the README. Glad that is working for you as well.

Cheers,
Arkadiy