BEDMS

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).

Installation

To install bedms use this command:

pip install bedms

or install the latest version from the GitHub repository:

pip install git+https://github.com/databio/bedms.git

Usage

from bedms import AttrStandardizer

model = AttrStandardizer("ENCODE")
results = model.standardize(pep="geo/gse228634:default")

assert results

To see the available schemas, you can run:

from bedms.constants import AVAILABLE_SCHEMAS
print(AVAILABLE_SCHEMAS)

# >> ['ENCODE', 'FAIRTRACKS', 'BEDBASE'] 

AVAILABLE_SCHEMAS is a list of available schemas that you can use to standardize your metadata.