Metadata-Version: 2.1
Name: bedshift
Version: 1.1.1
Summary: BED file perturbations
Home-page: https://bedshift.databio.org
Author: Aaron Gu
Author-email: ag5ym@virginia.edu
License: BSD2
Keywords: BED file,perturbation,bioinformatics,region set
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: System :: Distributed Computing
Description-Content-Type: text/markdown
Requires-Dist: logmuse
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: pyranges

# Bedshift

Docs: bedshift.databio.org

Install from PyPi: `pip install bedshift`

Install from local repository: `pip install .`

## Command line

Run with:

```
bedshift -l tests/hg38.chrom.sizes -b tests/test.bed
```

See `bedshift -h` for parameters.

## Python

```py
import bedshift

bedshifter = bedshift.Bedshift('tests/test.bed', 'hg38.chrom.sizes')
bedshifter.all_perturbations(addrate=0.3, addmean=320.0, addstdev=20.0,
							 shiftrate=0.3, shiftmean=-10.0, shiftstdev=120.0,
							 cutrate=0.1,
							 mergerate=0.11,
							 droprate=0.03)
# can also run single operations: shift, add, cut, merge, drop

bedshifter.to_bed('test_output.bed')
```



## Development

Run tests (from this directory):

```
python -m unittest
```

Double check the output files to see if the regions make sense.

build docs:





