Machine Learning Package for Microbiome

Dependencies

1. scikit-learn
2. click
3. pandas

Running the Commands

Bash completion

Empowered by click, microLearner supports bash auto-completion for command, subcommands, arguments and options. Users just need to run:

source bash_completion.sh

Or to make it permenant, add the above line to your ~/.bashrc file.

The bash_completion.sh file comes with the package. But you can also create or update it with the following command:

_MICROLEARNER_COMPLETE=source microLearner > bash_completion.sh

Other tips

1. microLearner supports shorthands for subcommands as long as the shorthand is unambiguous. For example, microLearner prep --help and microLearner preprocess --help are exactly the same.

2. microLearner is insensitive to the letter cases. For example, microLearner prep --help and MicroLearner Prep --HELP are exactly the same.

Preprocess

preprocess is the subcommand of microLearner. MinMaxScaler is the argument to the subcommand. --range, -o and -i are the options. The options for the command is insensitive to the letter cases.

microLearner preprocess MinMaxScaler --range 0 1 -i microLearner/data/otus.txt -o /tmp/foo.txt

microLearner preprocess MinMaxScaler --Range 0 1 -i microLearner/data/otus.txt -o /tmp/foo.txt

Classification

microLearner classify DecisionTreeClassifier --criterion entropy --max_features None --max_depth None --min_samples_split 2 --min_samples_leaf 1 --random_state None

microLearner classify DecisionTreeClassifier --criterion entropy --max_features None --max_depth None --min_samples_split 2 --min_samples_leaf 1 --random_state None

microLearner classify RandomForestClassifier --n_estimators 500

microLearner classify RandomForestClassifier 

Regression

microLearner regress

Clustering

microLearner cluster