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 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
from bedms import AttrStandardizer
model = AttrStandardizer("ENCODE")
results = model.standardize(pep="geo/gse228634:default")
assert resultsTo 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.