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
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:
Release files for bedshift 1.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| bedshift-1.1.1.tar.gz | 12.1 kB | Without provenance | Details for bedshift-1.1.1.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| bedshift-1.1.1-py3-none-any.whl | Python 3 | none | any | Details for bedshift-1.1.1-py3-none-any.whl |
Total release size: 24.0 kB
Release files / bedshift-1.1.1.tar.gz
| Download URL | bedshift-1.1.1.tar.gz |
|---|---|
| Size | 12.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
9507d30390f45dddddf53bef699004a237d18982d7e53b547825856e8c9ba0aa
|
|
BLAKE2b-256 checksum How to use checksums |
9945fb0183d5a987e1526aca06c7780a8239fb5b34a7d62d411a7fac575852db
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.1 importlib_metadata/3.10.1 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.60.0 CPython/3.9.4
|
Release files / bedshift-1.1.1-py3-none-any.whl
| Download URL | bedshift-1.1.1-py3-none-any.whl |
|---|---|
| Size | 11.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
c6777eb8c5f47d866a61ea3c973dad81f6e13ec3fffb84143af8982cbfdbc916
|
|
BLAKE2b-256 checksum How to use checksums |
17064733e31fd9e1bb34cc8b1b19e1caa5ca3da3e23c60173db9b686b3d5acfc
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.1 importlib_metadata/3.10.1 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.60.0 CPython/3.9.4
|
Security for bedshift 1.1.1
Provenance
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No provenance found
None of the files in this release were uploaded with provenance metadata.
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