{ "info": { "author": "Christian Ebeling", "author_email": "christian.ebeling@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": "PyUniProt |stable_build|\n========================\n\n|project_logo_large|\n\n|stable_documentation| |pypi_license|\n\n`PyUniProt `_ is a Python package\nto access and query UniProt data provided by the European Bioinformatics Institute (EMBL-EBI),\nthe SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR).\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.\nPyUniProt 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 pyUniProt 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`PyUniProt` 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 |pypi_version| |python_versions|\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nPyUniProt can be installed with `pip `_.\n\n.. code-block:: bash\n\n pip install pyuniprot\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 pyuniprot\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 pyuniprot\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 PyUniProt, 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 pyuniprot CHARACTER SET utf8 COLLATE utf8_general_ci;\n GRANT ALL PRIVILEGES ON pyuniprot.* TO 'pyuniprot_user'@'%' IDENTIFIED BY 'pyuniprot_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 pyuniprot 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 [pyuniprot_user]:\n MySQL/MariaDB password [pyuniprot_passwd]:\n database name [pyuniprot]:\n character set [utf8]:\n\nConnection will be tested and in case of success return `Connection was successful`.\nOtherwise you will see following hinte\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 pyuniprot\n pyuniprot.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 pyuniprot\n pyuniprot.set_mysql_connection(host='localhost', user='pyuniprot_user', passwd='pyuniprot_passwd', db='pyuniprot')\n\nUpdating\n~~~~~~~~\nThe updating process will download the *uniprot_sprot.xml.gz* file provided by the UniProt team on their ftp server\n`download page `_\n\n.. warning::\n\n Please note that UniProt download file needs ~700 Mb of disk space and the update takes ~2h only for\n human, mouse and rat (depending on your computer)\n\nIt is strongly recommended to restrict the entries liked to specific organisms your are interested in by parsing a list\nof NCBI Taxonomy IDs to the parameter `taxids`. To identify correct NCBI Taxonomy IDs please go to\n`NCBI Taxonomy web form `_. In the following example we use 9606 as identifier\nfor Homo sapiens, 10090 for Mus musculus and 10116 for Rattus norvegicus.\n\nThere are two options to import the data:\n\n1. Command line import\n\n .. code-block:: sh\n\n pyuniprot update --taxids 9606,10090,10116\n\n2. Python\n\n .. code-block:: python\n\n import pyuniprot\n pyuniprot.update(taxids=[9606, 10090, 10116])\n\nWe only recommend to import the whole UniProt dataset if you don't want to restrict your search. Import with no\nrestrictions will take several hours and take a lot of disk space.\n\nIf you want to load all UniProt entries in the database:\n\n.. code-block:: python\n\n import pyuniprot\n pyuniprot.update() # not recommended, please read the notes above\n\nThe update uses the download file if it still exists on you system (~/.pyuniprot/data/uniprot_sprot.xml.gz). If you use\nthe parameter `force_download` the current file from UniProt will be downloaded.\n\n.. code-block:: python\n\n import pyuniprot\n pyuniprot.update(force_download=True, taxids=[9606, 10090, 10116])\n\nQuick start with query functions\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nInitialize the query object\n\n.. code-block:: python\n\n query = pyuniprot.query()\n\nGet all entries\n\n.. code-block:: python\n\n all_entries = query.entry()\n\n\nUse parameters like gene_name to find specific entries\n\n.. code-block:: python\n\n >>> entry = query.entry(gene_name='YWHAE', taxid=9606, recommended_short_name='14-3-3E', name='1433E_HUMAN')[0]\n >>> entry\n 14-3-3 protein epsilon\n\nEntry is the root element in the database. Form here you can reach all other data\n >>> entry.accessions\n [P62258, B3KY71, D3DTH5, P29360, P42655, Q4VJB6, Q53XZ5, Q63631, Q7M4R4]\n >>> entry.functions\n [\"Adapter protein implicated in the regulation of a large spectrum of both ...\"]\n\nIf a parameter ends on a **s** you can search\n >>> alcohol_dehydrogenases = q.entry(ec_numbers='1.1.1.1')\n >>> [x.name for x in q.get_entry(ec_numbers='1.1.1.1')]\n ['ADHX_RAT', 'ADH1_RAT', 'ADHX_HUMAN', 'ADHX_MOUSE']\n >>> query.entry(ec_numbers=('1.1.1.1', '1.1.1.2'))\n ['Adh5', 'Adh1', 'ADH5', 'Adh5', 'Adh6', 'ADH7', 'Adh7', 'Adh7', 'Adh1']\n\nAs dataframe with a limit of 10 and accession number starts with Q9 (% used as wildcard)\n\n.. code-block:: python\n\n >>> query.accession(as_df=True, limit=3, accession='Q9%')\n id accession entry_id\n 0 1 Q9CQV8 1\n 1 32 Q9GIK8 6\n 2 33 Q9TQB4 6\n\nFull documentation on query function you will find\n`here `_\n\nMore information\n----------------\nSee the `installation documentation `_ for more advanced\ninstructions. Also, check the change log at :code:`CHANGELOG.rst`.\n\nUniProt tools and licence (use of data)\n---------------------------------------\nUniProt provides also many online `query interfaces `_ on their website.\n\nPlease be aware of the `UniProt licence `_.\n\nLinks\n-----\nUniversal Protein Resource (UniProt)\n\n- `UniProt website `_\n- `About UniProt `_\n\nPyUniProt\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://api.travis-ci.org/cebel/pyuniprot.svg?branch=master\n :target: https://travis-ci.org/cebel/pyuniprot\n :alt: Stable Build Status\n\n.. |stable_documentation| image:: https://readthedocs.org/projects/pyuniprot/badge/?version=latest\n :target: http://pyuniprot.readthedocs.io/en/latest/\n :alt: Development Documentation Status\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/pyuniprot.svg\n :alt: Apache 2.0 License\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/pyuniprot.svg\n :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/pyuniprot.svg\n :alt: Current version on PyPI\n\n.. |phago_logo| image:: https://raw.githubusercontent.com/cebel/pyuniprot/master/docs/source/_static/logos/phago_logo.jpeg\n :target: https://www.imi.europa.eu/content/phago\n :alt: PHAGO project logo\n\n.. |aetionomy_logo| image:: https://raw.githubusercontent.com/cebel/pyuniprot/master/docs/source/_static/logos/aetionomy_logo.png\n :target: http://www.aetionomy.eu/en/vision.html\n :alt: AETIONOMY project logo\n\n.. |imi_logo| image:: https://raw.githubusercontent.com/cebel/pyuniprot/master/docs/source/_static/logos/imi_logo.png\n :target: https://www.imi.europa.eu/\n :alt: IMI project logo\n\n.. |scai_logo| image:: https://raw.githubusercontent.com/cebel/pyuniprot/master/docs/source/_static/logos/scai_logo.png\n :target: 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