bedms

Name	bedms JSON
Version	0.1.0 JSON
	download
home_page	https://github.com/databio/bedmess/
Summary	BEDMess attribute standardizer for metadata attribute standardization
upload_time	2024-09-16 19:27:07
maintainer	None
docs_url	None
author	Saanika Tambe
requires_python	None
license	BSD2
keywords	project metadata bioinformatics
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # 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.

            

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