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        "author": "Patrik Kaura",
        "author_email": "patrikkaura@gmail.com",
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        "classifiers": [
            "Intended Audience :: Education",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3.8",
            "Programming Language :: Python :: 3.9",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "<div align=\"center\">\n    <img src=\"https://gitlab.com/PatrikKaura/dna_analyser_ibp_logos/-/raw/master/logo.png\" alt='logo' width='300px'>\n    <br/>\n    <br/>\n    <a href=\"https://gitlab.com/PatrikKaura/DNA_analyser_IBP/-/commits/master\">\n        <img alt=\"pipeline status\" src=\"https://gitlab.com/PatrikKaura/DNA_analyser_IBP/badges/master/pipeline.svg\" />\n    </a>\n    <a href=\"https://pypi.org/project/dna-analyser-ibp/\">\n        <img src=\"https://img.shields.io/badge/version-3.4.1-brightgreen.svg\" alt='version'/>\n    </a>\n    <img src=\"https://img.shields.io/badge/python-3.6-brightgreen.svg\" alt='python_version'/>\n    <img src=\"https://img.shields.io/badge/python-3.7-brightgreen.svg\" alt='python_version'/>\n    <img src=\"https://img.shields.io/badge/python-3.8-brightgreen.svg\" alt='python_version'/>\n    <a href=\"https://choosealicense.com/licenses/gpl-3.0/\">\n        <img src='https://img.shields.io/badge/licence-GNU%20v3.0-blue.svg' alt='licence'/>\n    </a>\n    <h1 align='center'> DNA analyser IBP </h1>\n</div>\n\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 >= 3.6\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\n## Documentation\n\nMethods are documented in the following [documentation](https://patrikkaura.gitlab.io/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* tenacity >= 6.1.0\n* requests >= 2.20\n* requests-toolbelt >= 0.9.1\n* pyjwt >= 1.7.1\n* pandas >= 0.23\n* matplotlib >= 3.0.3\n* tqdm >= 4.28\n\n## DEV dependencies\n\n* pytest = \"^6.0.2\"\n* pdoc3 = \"^0.9.1\"\n* black = \"^20.0\"\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://gitlab.com/PatrikKaura/)\n* **Jan Kolomaznik** - *Supervisor* - [jankolomaznik](https://github.com/Kolomaznik)\n* **Ji\u0159\u00ed \u0160\u0165astn\u00fd** - *Supervisor*\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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