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updated readme
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khoroshevskyi committed Sep 13, 2024
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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.
```
AVAILABLE_SCHEMAS is a list of available schemas that you can use to standardize your metadata.

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