<h1 align='center'> DNA analyser IBP </h1>
<br />
<div align="center">
<a href="https://pypi.org/project/dna-analyser-ibp/">
<img src="https://img.shields.io/badge/Version 3.6.0-green?style=for-the-badge" alt='package_version'/>
</a>
<img src="https://img.shields.io/badge/Python 3.10+-00599C?style=for-the-badge&logo=python&logoColor=white" alt='python_version'/>
<img src="https://img.shields.io/badge/jupyter-gray?style=for-the-badge&logo=jupyter" alt='jupyter'/>
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<img src="https://img.shields.io/badge/gnu-white?style=for-the-badge&logo=gnu&logoColor=black" alt='licence'/>
</a>
</div>
<br />
Tool for creating R-loop tracker, P53predictor, G4Killer and G4Hunter analysis. Work as API wrapper for IBP DNA analyzer API [bioinformatics.ibp](http://bioinformatics.ibp.cz/).
Currently working with an instance of DNA analyser server running on http://bioinformatics.ibp.cz computational core but can be switched
to the local instance of the server.
# Getting Started
## Prerequisites
python >= 3.10
## Installing
To install test version from [Pypi](https://pypi.org/project/dna-analyser-ibp/).
```commandline
pipenv install dna-analyser-ibp
```
```commandline
pip install dna-analyser-ibp
```
## Quick start
DNA analyser uses `pandas.Dataframe` or `pandas.Series`. Firstly the user has to create `Api` object and login to API.
```python
from DNA_analyser_IBP.api import Api
API = Api()
```
```python
Enter your email example@example.cz
Enter your password ········
2020-09-16 18:51:17.943398 [INFO]: User host is trying to login ...
2020-09-16 18:51:17.990580 [INFO]: User host is successfully loged in ...
```
If DNA analyser API server is not running on http://bioinformatics.ibp.cz then you have to set server paramether to create `Api` object.
```python
from DNA_analyser_IBP.api import Api
API = Api(
server='http://hostname:port/api'
)
```
## Sequence uploading
Sequences can be uploaded from NCBI, plain text or text file. Example bellow illustrates NCBI sequence uploading `Homo sapiens chromosome 12`.
```python
API.sequence.ncbi_creator(
circular= True,
tags=['Homo','sapiens', 'chromosome'],
name='Homo sapiens chromosome 12',
ncbi_id='NC_000012.12'
)
API.sequence.load_all(
tags=['Homo']
)
```
## G4Hunter
G4Hunter is a tool for prediction of G-quadruplex propensity in nucleic acids, this algorithm considers G-richness and G-skewness of a tested sequence and shows a quadruplex propensity score.
```python
sapiens = API.g4hunter.load_all(
tags=['Homo']
)
API.g4hunter.analyse_creator(
sequence=sapiens,
tags=['analyse','Homo', 'sapiens'],
threshold=1.4,
window_size=30
)
```
To load results of G4Hunter analysis.
```python
API.g4hunter.load_all(
tags=['analyse', 'Homo', 'sapiens']
)
```
## R-loop tracker
R-loop tracker is a toll for prediction of R-loops in nucleic acids. The algorithms search for R-loop initiation zone based on presence of G-clusters and R-loop elongation zone containing at least 40% of Guanine density.
```python
sapiens = API.g4hunter.load_all(
tags=['Homo']
)
API.rloopr.analyse_creator(
sequence=sapiens,
tags=['analyse', 'Homo', 'sapiens'],
riz_2g_cluster=True,
riz_3g_cluster=False
)
```
To load results of R-loop tracker analysis.
```python
API.rloopr.load_all(
tags=['analyse', 'Homo', 'sapiens']
)
```
## G4Killer
G4Killer algorithm allows to mutate DNA sequences with desired G4Hunter score with minimal mutation steps.
```python
API.g4killer.run(
sequence='AATTATTTGGAAAGGGGGGGTTTTCCGA',
threshold=0.5
)
API.g4killer.run_multiple(
sequences=[
'AATTATTTGGAAAGGGGGGGTTTTCCGA',
'AATTATTTGGAAAGGGGGGGTTTTCCGA'
],
threshold=0.5
)
```
## P53 predictor
P53 binding predictor for 20 base pairs sequences.
```python
API.p53.run(
sequence='GGACATGCCCGGGCATGTCC'
)
API.p53.run_multiple(
sequences=[
'GGACATGCCCGGGCATGTCC',
'GGACATGCCCGGGCATGTCC'
]
)
```
# Development
## Dependencies
* requests = "2.31.0"
* pandas = "2.0.0"
* tqdm = "4.66.0"
* pyjwt = "2.8.0"
* matplotlib = "3.7.2"
* requests-toolbelt = "1.0.0"
* tenacity = "8.2.3"
## DEV dependencies
* pytest = "7.4.2"
## Tests
To run tests only when downloaded directly from this repository.
```commandline
pytest -v tests/
```
## Authors
* **Patrik Kaura** - *Main developer* - [patrikkaura](https://github.com/patrikkaura)
## License
This project is licensed under the GPL-3.0 License - see the [LICENSE.md](LICENSE.md) file for details.
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"description": "<h1 align='center'> DNA analyser IBP </h1>\n<br />\n<div align=\"center\">\n <a href=\"https://pypi.org/project/dna-analyser-ibp/\">\n <img src=\"https://img.shields.io/badge/Version 3.6.0-green?style=for-the-badge\" alt='package_version'/>\n </a>\n <img src=\"https://img.shields.io/badge/Python 3.10+-00599C?style=for-the-badge&logo=python&logoColor=white\" alt='python_version'/>\n <img src=\"https://img.shields.io/badge/jupyter-gray?style=for-the-badge&logo=jupyter\" alt='jupyter'/>\n <a href=\"https://choosealicense.com/licenses/gpl-3.0/\">\n <img src=\"https://img.shields.io/badge/gnu-white?style=for-the-badge&logo=gnu&logoColor=black\" alt='licence'/>\n </a>\n</div>\n<br />\n\nTool for creating R-loop tracker, P53predictor, G4Killer and G4Hunter analysis. Work as API wrapper for IBP DNA analyzer API [bioinformatics.ibp](http://bioinformatics.ibp.cz/).\nCurrently working with an instance of DNA analyser server running on http://bioinformatics.ibp.cz computational core but can be switched \nto the local instance of the server.\n\n# Getting Started\n\n## Prerequisites\n\npython >= 3.10\n\n## Installing\n\nTo install test version from [Pypi](https://pypi.org/project/dna-analyser-ibp/).\n\n```commandline\npipenv install dna-analyser-ibp\n```\n\n```commandline\npip install dna-analyser-ibp\n```\n## Quick start\n\nDNA analyser uses `pandas.Dataframe` or `pandas.Series`. Firstly the user has to create `Api` object and login to API.\n```python\nfrom DNA_analyser_IBP.api import Api\n\nAPI = Api()\n```\n```python\nEnter your email example@example.cz\nEnter your password \u00b7\u00b7\u00b7\u00b7\u00b7\u00b7\u00b7\u00b7\n\n2020-09-16 18:51:17.943398 [INFO]: User host is trying to login ...\n2020-09-16 18:51:17.990580 [INFO]: User host is successfully loged in ...\n```\nIf DNA analyser API server is not running on http://bioinformatics.ibp.cz then you have to set server paramether to create `Api` object.\n```python\nfrom DNA_analyser_IBP.api import Api\n\nAPI = Api(\n server='http://hostname:port/api'\n)\n```\n\n## Sequence uploading\nSequences can be uploaded from NCBI, plain text or text file. Example bellow illustrates NCBI sequence uploading `Homo sapiens chromosome 12`.\n```python\nAPI.sequence.ncbi_creator(\n circular= True,\n tags=['Homo','sapiens', 'chromosome'],\n name='Homo sapiens chromosome 12',\n ncbi_id='NC_000012.12'\n)\n\nAPI.sequence.load_all(\n tags=['Homo']\n)\n```\n\n## G4Hunter\nG4Hunter is a tool for prediction of G-quadruplex propensity in nucleic acids, this algorithm considers G-richness and G-skewness of a tested sequence and shows a quadruplex propensity score. \n```python\nsapiens = API.g4hunter.load_all(\n tags=['Homo']\n)\n\nAPI.g4hunter.analyse_creator(\n sequence=sapiens,\n tags=['analyse','Homo', 'sapiens'],\n threshold=1.4,\n window_size=30\n)\n```\nTo load results of G4Hunter analysis.\n```python\nAPI.g4hunter.load_all(\n tags=['analyse', 'Homo', 'sapiens']\n) \n```\n\n## R-loop tracker\n R-loop tracker is a toll for prediction of R-loops in nucleic acids. The algorithms search for R-loop initiation zone based on presence of G-clusters and R-loop elongation zone containing at least 40% of Guanine density.\n```python\nsapiens = API.g4hunter.load_all(\n tags=['Homo']\n)\nAPI.rloopr.analyse_creator(\n sequence=sapiens,\n tags=['analyse', 'Homo', 'sapiens'],\n riz_2g_cluster=True,\n riz_3g_cluster=False\n)\n```\nTo load results of R-loop tracker analysis.\n```python\nAPI.rloopr.load_all(\n tags=['analyse', 'Homo', 'sapiens']\n) \n```\n\n## G4Killer\nG4Killer algorithm allows to mutate DNA sequences with desired G4Hunter score with minimal mutation steps.\n```python\nAPI.g4killer.run(\n sequence='AATTATTTGGAAAGGGGGGGTTTTCCGA',\n threshold=0.5\n) \n\nAPI.g4killer.run_multiple(\n sequences=[\n 'AATTATTTGGAAAGGGGGGGTTTTCCGA',\n 'AATTATTTGGAAAGGGGGGGTTTTCCGA'\n ],\n threshold=0.5\n)\n```\n## P53 predictor\nP53 binding predictor for 20 base pairs sequences. \n```python\nAPI.p53.run(\n sequence='GGACATGCCCGGGCATGTCC'\n)\n\nAPI.p53.run_multiple(\n sequences=[\n 'GGACATGCCCGGGCATGTCC',\n 'GGACATGCCCGGGCATGTCC'\n ]\n) \n```\n\n# Development\n\n## Dependencies\n\n* requests = \"2.31.0\"\n* pandas = \"2.0.0\"\n* tqdm = \"4.66.0\"\n* pyjwt = \"2.8.0\"\n* matplotlib = \"3.7.2\"\n* requests-toolbelt = \"1.0.0\"\n* tenacity = \"8.2.3\"\n\n## DEV dependencies\n\n* pytest = \"7.4.2\"\n\n\n## Tests\n\nTo run tests only when downloaded directly from this repository.\n\n```commandline\npytest -v tests/\n```\n\n## Authors\n\n* **Patrik Kaura** - *Main developer* - [patrikkaura](https://github.com/patrikkaura)\n\n## License\n\nThis project is licensed under the GPL-3.0 License - see the [LICENSE.md](LICENSE.md) file for details.\n",
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