{ "info": { "author": "Andrej Konotopez", "author_email": "Andrej.Konotopez@scai.fraunhofer.de", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Database", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "|project_logo_large| |stable_build| |stable_documentation| |pypi_license|\n=========================================================================\n\n`PyHGNC `_ is a Python package\nto access and query data provided by HGNC-approved gene nomenclature, gene families and associated resources \nincluding links to genomic, proteomic and phenotypic information.\n\nData are installed in a (local or remote) RDBMS enabling bioinformatic algorithms very fast response times\nto sophisticated queries and high flexibility by using SOLAlchemy database layer.\n\nPyHGNC is developed by the\n`Department of Bioinformatics `_\nat the Fraunhofer Institute for Algorithms and Scientific Computing\n`SCAI `_\nFor more in for information about PyHGNC go to\n`the documentation `_.\n\n|er_model|\n\nThis development is supported by following `IMI `_ projects:\n\n- `AETIONOMY `_ and\n- `PHAGO `_.\n\n|imi_logo| |aetionomy_logo| |phago_logo| |scai_logo|\n\nSupported databases\n-------------------\n\n`PyHGNC` uses `SQLAlchemy `_ to cover a wide spectrum of RDMSs\n(Relational database management system). For best performance MySQL or MariaDB is recommended. But if you have no\npossibility to install software on your system SQLite - which needs no further\ninstallation - also works. Following RDMSs are supported (by SQLAlchemy):\n\n1. `Firebird `_\n2. `Microsoft SQL Server `_\n3. `MySQL `_ / `MariaDB `_\n4. `Oracle `_\n5. `PostgreSQL `_\n6. `SQLite `_\n7. Sybase\n\nGetting Started\n---------------\nThis is a quick start tutorial for impatient.\n\nInstallation\n~~~~~~~~~~~~\n|pypi_version| |python_versions|\n\nPyHGNC can be installed with `pip `_.\n\n.. code-block:: bash\n\n pip install pyhgnc\n\nIf you fail because you have no rights to install use superuser (sudo on Linux before the commend) or ...\n\n.. code-block:: bash\n\n pip install --user pyhgnc\n\nIf you want to make sure you are installing this under python3 use ...\n\n.. code-block:: bash\n\n python3 -m pip install pyhgnc\n\nSQLite\n~~~~~~\n.. note:: If you want to use SQLite as your database system, because you ...\n\n - have no possibility to use RDMSs like MySQL/MariaDB\n - just test PyHGNC, but don't want to spend time in setting up a database\n\n skip the next *MySQL/MariaDB setup* section. But in general we strongly recommend MySQL or MariaDB as your\n relational database management system.\n\nIf you don't know what all that means skip the section *MySQL/MariaDB setup*.\n\nDon't worry! You can always later change the configuration. For more information about\nchanging database system later go to the subtitle *Changing database configuration*\n`Changing database configuration `_\nin the documentation on readthedocs.\n\nMySQL/MariaDB setup\n~~~~~~~~~~~~~~~~~~~\nLog in MySQL as root user and create a new database, create a user, assign the rights and flush privileges.\n\n.. code-block:: mysql\n\n CREATE DATABASE pyhgnc CHARACTER SET utf8 COLLATE utf8_general_ci;\n GRANT ALL PRIVILEGES ON pyhgnc.* TO 'pyhgnc_user'@'%' IDENTIFIED BY 'pyhgnc_passwd';\n FLUSH PRIVILEGES;\n\nThere are two options to set the MySQL/MariaDB.\n\n1. The simplest is to start the command line tool\n\n.. code-block:: sh\n\n pyhgnc mysql\n\nYou will be guided with input prompts. Accept the default value in squared brackets with RETURN. You will see\nsomething like this\n\n.. code-block:: sh\n\n server name/ IP address database is hosted [localhost]:\n MySQL/MariaDB user [pyhgnc_user]:\n MySQL/MariaDB password [pyhgnc_passwd]:\n database name [pyhgnc]:\n character set [utf8]:\n\nConnection will be tested and in case of success return `Connection was successful`.\nOtherwise you will see following hint\n\n.. code-block:: sh\n\n Test was NOT successful\n\n Please use one of the following connection schemas\n MySQL/MariaDB (strongly recommended):\n mysql+pymysql://user:passwd@localhost/database?charset=utf8\n\n PostgreSQL:\n postgresql://user:passwd@localhost/database\n\n MsSQL (pyodbc needed):\n mssql+pyodbc://user:passwd@database\n\n SQLite (always works):\n\n - Linux:\n sqlite:////absolute/path/to/database.db\n\n - Windows:\n sqlite:///C:\\absolute\\path\\to\\database.db\n\n Oracle:\n oracle://user:passwd@localhost:1521/database\n\n2. The second option is to start a python shell and set the MySQL configuration.\nIf you have not changed anything in the SQL statements above ...\n\n.. code-block:: python\n\n import pyhgnc\n pyhgnc.set_mysql_connection()\n\nIf you have used you own settings, please adapt the following command to you requirements.\n\n.. code-block:: python\n\n import pyhgnc\n pyhgnc.set_mysql_connection(host='localhost', user='pyhgnc_user', passwd='pyhgnc_passwd', db='pyhgnc')\n\nUpdating\n~~~~~~~~\nThe updating process will download the complete HGNC json file and the HCOP file.\n\n.. code-block:: python\n\n import pyhgnc\n pyhgnc.manager.database.update()\n\nThis will use either the default connection settings of PyHGNC or the settings defined by the user.\nIt is also possible to run the update process from shell.\n\n.. code-block:: sh\n\n pyhgnc update\n\nQuick start with query functions\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nInitialize the query object\n\n.. code-block:: python\n\n query = pyhgnc.query()\n\nGet all HGNC entries:\n\n.. code-block:: python\n\n all_entries = query.hgnc()\n\n.. hint::\n Check out the documentation: Query functions section for more examples and check out the Query section for\n all possible parameters for the different models.\n\nMore information\n----------------\nSee the `installation documentation `_ for more advanced\ninstructions. Also, check the change log at :code:`CHANGELOG.rst`.\n\nHGNC tools\n----------\nHGNC provides also `online tools `_ .\n\nLinks\n-----\nHUGO Gene Nomenclature Committee (HGNC)\n\n- `HGNC website `_\n\nPyHGNC\n\n- Documented on `Read the Docs `_\n- Versioned on `GitHub `_\n- Tested on `Travis CI `_\n- Distributed by `PyPI `_\n- Chat on `Gitter `_\n\n.. |stable_build| image:: https://travis-ci.org/LeKono/pyhgnc.svg?branch=master\n :target: https://travis-ci.org/LeKono/pyhgnc\n :alt: Stable Build Status\n\n.. |stable_documentation| image:: https://readthedocs.org/projects/pyhgnc/badge/?version=latest\n :target: http://pyhgnc.readthedocs.io/en/latest/\n :alt: Development Documentation Status\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/PyHGNC.svg\n :alt: Apache 2.0 License\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/PyHGNC.svg\n :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/PyHGNC.svg\n :alt: 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