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
Description: # 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:
        
        
        
        
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
