Metadata-Version: 2.1
Name: bedms
Version: 0.1.0
Summary: BEDMess attribute standardizer for metadata attribute standardization
Home-page: https://github.com/databio/bedmess/
Author: Saanika Tambe
License: BSD2
Keywords: project,metadata,bioinformatics
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: torch
Requires-Dist: sentence-transformers
Requires-Dist: pephubclient>=0.4.2
Requires-Dist: peppy>=0.40.6

# 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

```python
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.
