diff --git a/README.md b/README.md index defcf09..676ecbb 100644 --- a/README.md +++ b/README.md @@ -3,41 +3,35 @@ BEDMS (BED Metadata Standardizer) is a tool used to standardize genomics/epigenomics metadata based on a schema chosen by the user ( eg. ENCODE, FAIRTRACKS, BEDBASE). -To install `attribute-standardizer` , you need to clone this repository first. Follow the steps given below to install: +## Installation +To install `bbclient` use this command: ``` -git clone https://github.com/databio/bedms.git - -cd bedms - -pip install . - +pip install bedms +``` +or install the latest version from the GitHub repository: +``` +pip install git+https://github.com/databio/bedms.git ``` ## Usage -Using Python, this is how you can run `attribute_standardizer` and print the results : - - -``` +```python from bedms import AttrStandardizer model = AttrStandardizer("ENCODE") -model = AttrStandardizer("FAIRTRACKS") - -results = model.standardize(pep ="geo/gse178283:default") - -print(results) +results = model.standardize(pep="geo/gse228634:default") +assert results ``` -To see the available schemas, you can run: -``` -schemas = model.get_available_schemas() -print(schemas) +To see the available schemas, you can run: ``` +from bedms.constants import AVAILABLE_SCHEMAS +print(AVAILABLE_SCHEMAS) -This will print the available schemas as a list. +# >> ['ENCODE', 'FAIRTRACKS', 'BEDBASE'] -You can use the format provided in the `trial.py` script in this repository as a reference. \ No newline at end of file +``` +AVAILABLE_SCHEMAS is a list of available schemas that you can use to standardize your metadata.