Metadata-Version: 2.1
Name: pybioinformatic
Version: 0.0.2
Summary: Bioinformatic python package.
Author-email: Wenlin Xu <wenlinxu.njfu@outlook.com>
Project-URL: Homepage, https://github.com/wenlinXu-njfu/Leo
Project-URL: Bug Tracker, https://github.com/wenlinXu-njfu/Leo/issues
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENCE
Requires-Dist: click>=8.1.7
Requires-Dist: matplotlib>=3.7.5
Requires-Dist: natsort>=8.4.0
Requires-Dist: openpyxl>=3.1.2
Requires-Dist: pandas>=2.0.3
Requires-Dist: seaborn>=0.13.2
Requires-Dist: tqdm>=4.66.2
Requires-Dist: typing_extensions>=4.9.0
Requires-Dist: ViennaRNA>=2.6.4
Requires-Dist: xlrd>=2.0.1
Requires-Dist: xlsxwriter>=3.2.0
Requires-Dist: xlwt>=1.3.0

# This is a bioinformatic python package.

## Install
```shell
pip install pybioinformatic --upgrade
```

## Usage example
### RNA secondary structure prediction.
```python
from pybioinformatic import Nucleotide

# Generate random nucleic acid sequence.
random_nucl = Nucleotide.random_nucl(name='demo', length=[100, 150], bias=1.0)

# Secondary structure prediction
ss, mfe = random_nucl.predict_secondary_structure('test/structure.ps')
print(ss, mfe, sep='\n')
```
```
>demo length=135
CAAAAAAAAACCATAAGCCGCCATGTCTCACATCGCAACCGGCTCAAGTAGAGTGCCCCTAATAATATGATCTTCGCTACAGAAGTTCCCCCCCCGCTGCCGGCTAGATGCGAACTCCACGCCTGGATGGCTCAG
...............((((((((.((......(((((.(.((((...((((.................((.((((......)))).))........)))).)))).).))))).......)).))).)))))...
-27.299999237060547
```
![image](test/structure.png)
