https://github.com/databio/bedshift

Bedfile perturbation tool
https://github.com/databio/bedshift

genomic-intervals genomic-regions region-of-interest

Last synced: about 2 months ago
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Bedfile perturbation tool

• Host: GitHub
• URL: https://github.com/databio/bedshift
• Owner: databio
• License: bsd-2-clause
• Created: 2019-10-11T00:55:50.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2023-12-09T21:52:05.000Z (about 1 year ago)
• Last Synced: 2024-09-12T04:08:15.087Z (4 months ago)
• Topics: genomic-intervals, genomic-regions, region-of-interest
• Language: Python
• Homepage: http://bedshift.databio.org
• Size: 728 KB
• Stars: 16
• Watchers: 16
• Forks: 2
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
# 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: