Bedshift
Bedshift is a tool for randomly perturbing BED file regions. The perturbations supported on regions are shift, drop, add, cut, and merge. This tool is particularly useful for creating test datasets for various tasks, since there often is no ground truth dataset to compare to. By perturbing a file, a pipeline or analysis can be run on both the perturbed file and the original file, then be compared.
Installing
The package is available for public download on PyPi.
pip install bedshift
Quickstart
The package is available for use both as a command line interface and a python package. To get started, type on the command line:
bedshift -h
The following examples will shift 10% of the regions and add 10% new regions in examples/test.bed. The -l argument is the file in which chromosome sizes are located, and is only required for adding and/or shifting regions. The output is located at bedshifted_test.bed.
CLI:
bedshift -l hg38.chrom.sizes -b tests/test.bed -s 0.1 -a 0.1
Python:
import bedshift
bedshifter = bedshift.Bedshift('tests/test.bed', 'hg38.chrom.sizes')
bedshifter.shift(shiftrate=0.1, shiftmean=0.0, shiftstdev=120.0)
bedshifter.add(addrate=0.1, addmean=320.0, addstdev=20.0)
bedshifter.to_bed('tests/test_output.bed')
Example Repository
If you're looking to use Bedshift in your own experiment, we created an example repository containing working code to:
- Produce a large dataset of Bedshift files
- Run a pipeline on the dataset and obtain results
- Aggregate and visualize the results
It integrates the PEP and looper workflow allowing you to easily run the project out of the box.