Metadata-Version: 2.4
Name: bits-yoshi
Version: 0.2.1
Summary: miscellaneous BioInformatics ToolS
Author-email: Yoshihiko Suzuki <yoshi.suzuki.1992@gmail.com>
License: MIT License
        
        Copyright (c) 2018 Yoshihiko Suzuki
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/yoshihikosuzuki/bits
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: logzero
Requires-Dist: edlib
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: pyfastx
Requires-Dist: pysam
Requires-Dist: igv-notebook
Requires-Dist: plotly_light>=1.0
Dynamic: license-file

# BITS: miscellaneous BioInformatics ToolS

Basically bioinformatics-related, reusable Python3 codes as a package.

## How to install

```bash
git clone https://github.com/yoshihikosuzuki/bits
cd bits
pip install .
```

To run unit tests,

```bash
python -m unittest
```

## Optional requirements

If you use `bits.seq.load_fast[a|q]` with `range=` option,

- [Seqkit](https://bioinf.shenwei.me/seqkit/)

If you use `bits.seq.DotPlot`,

- [Gepard](https://github.com/univieCUBE/gepard), or
- [modified Gepard](https://github.com/yoshihikosuzuki/gepard) (recommended)

If you use `bits.seq.load_db` etc.,

- [DAZZ_DB](https://github.com/thegenemyers/DAZZ_DB)

## How to use

BITS has two submodules:

- `bits.seq` for DNA sequence manipulations, and
- `bits.util` for other, general purposes in Python programming.

Import and use any function/class as follows:

```python
import bits.seq as bs

print(bs.revcomp_seq('aactg'))
```

```text
> cagtt
```
