BiasAway
a tool to generate composition-matched background sequence sets
Documentation
A detailed documentation is available in different formats: HTML | PDF | ePUB
Installation
Quick installation using conda
BiasAway is available on Bioconda for installation via conda.
conda install -c bioconda biasawayInstall using pip
BiasAway is also available on PyPi for installation via pip.
pip install biasawayBiasAway is developed in Python and Python packages biopython and numpy. Both pip and conda will install these dependencies and you are ready to use BiasAway. It is tested with Python versions 3.4, 3.5, 3.6, and 3.7.
Install BiasAway from source
You can install a development version by using git from bitbucket.
Install development version from Bitbucket
If you have git installed, use this:
git clone https://bitbucket.org/CBGR/biasaway.git
cd biasaway
python setup.py sdist installHow to use BiasAway
Once you have installed biasaway, you can type:
biasaway --helpThis will show the main help, which lists the four subcommands/modules: k, w, g, and c.
usage: biasaway <subcommand> [options]
positional arguments <subcommand>: {k,w,g,c}
List of subcommands
k k-mer shuffling generator
w k-mer shuffling within a sliding window generator
g %GC distribution-based background chooser
c GC distribution and %GC composition within a sliding window background chooser
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exitAnd to view the help for the six subcommands k, w, g, and c type:
biasaway k --help
biasaway w --help
biasaway g --help
biasaway c --helpInteractive web-server
BiasAway web-server is freely available at: http://biasaway.uio.no
Support
If you have questions, or found any bug in the program, please write to us at azizk[at]uio.no or anthony.mathelier[at]ncmm.uio.no
Release files for biasaway 3.3.0
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 | |
|---|---|---|---|---|
| biasaway-3.3.0.tar.gz | 27.8 kB | Without provenance | Details |
Release files / biasaway-3.3.0.tar.gz
| Download URL | biasaway-3.3.0.tar.gz |
|---|---|
| Size | 27.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
6f7396be4a5d53a86c706218a0e611fe31f82a5f0cf5d7f0a15ba5ad02aa9523
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No |
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twine/3.1.1 pkginfo/1.5.0.1 requests/2.24.0 setuptools/49.6.0.post20200917 requests-toolbelt/0.9.1 tqdm/4.49.0 CPython/3.7.8
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Security for biasaway 3.3.0
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