Mothulity

Enhancements

14

- --cluster-method gives an opportunity to use OTU clustering differently just with opticlust default value. Among other method, there are --cluster-method agc and --cluster-method dgc which implement [Vsearch](https://github.com/torognes/vsearch) - an open-source alternative to [usearch](https://www.drive5.com/usearch/), so it should be way more efficient.

Updates

- conda environment file, not only containing [Vsearch](https://github.com/torognes/vsearch) but also generated with conda v4.5.1

Updates

10

- README changes address the need for the description of new config-file-database-path-related features from [v1.4.0](https://github.com/dizak/mothulity/tree/v1.4.0)

Enhancements

10

- mothulity.py handles default databases paths with config file.
- mothulity --set-align-database-path and mothulity.py --set-taxonomy-database-path should be used for that rather than editing the config file by hand.
- Default paths are set during installation.

Updates

- Code inside mothulity_dbaser.py is way cleaner.

Fixes

8

- mothulity_dbaser.py downloads all databases in a row, skipping bad connections.

ENH: Changed mothulity_dbaser CLI to take positional argument.

ENH: First unittests.

ENH: Setting databases paths in config file with mothulity CLI.

UPD: Code comments and restructuring.

UPD

- README

FIX
- removed shelve caching-related code
UPD
- depeding on system-wide mothur instalation if using MPI