{ "info": { "author": "Jan P Buchmann", "author_email": "jpb@members.fsf.org", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", "Operating System :: OS Independent", "Programming Language :: Python :: 3.6", "Topic :: Database", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries" ], "description": ".. image:: https://readthedocs.org/projects/entrezpy/badge/?version=master\n :target: https://entrezpy.readthedocs.io/en/master/?badge=master\n :alt: Documentation Status\n\n.. image:: https://img.shields.io/pypi/pyversions/entrezpy.svg?style=popout-square\n :alt: PyPI - Python Version\n\n.. image:: https://img.shields.io/pypi/l/entrezpy.svg?style=popout-square\n :alt: PyPI - License\n\n.. image:: https://img.shields.io/pypi/v/entrezpy.svg?style=popout-square\n :alt: PyPI\n\n.. image:: https://img.shields.io/pypi/format/entrezpy.svg?style=popout-square\n :alt: PyPI - Format\n\n.. image:: https://img.shields.io/pypi/status/entrezpy.svg?style=popout-square\n :alt: PyPI - Status\n\nEntrezpy README\n===============\n\nSynopsis\n--------\n\n.. code::\n\n $ pip install entrezpy --user\n\n>>> import entrezpy.conduit\n>>> w = entrezpy.conduit.Conduit('myemail')\n>>> fetch_influenza = w.new_pipeline()\n>>> sid = fetch_influenza.add_search({'db' : 'nucleotide', 'term' : 'H3N2 [organism] AND HA', 'rettype':'count', 'sort' : 'Date Released', 'mindate': 2000, 'maxdate':2019, 'datetype' : 'pdat'})\n>>> fid = fetch_influenza.add_fetch({'retmax' : 10, 'retmode' : 'text', 'rettype': 'fasta'}, dependency=sid)\n>>> w.run(fetch_influenza)\n\nEntrezpy is a dedicated Python library to interact with NCBI_ Entrez\ndatabases [Entrez2016]_ via the E-Utilities ([Sayers2018]_, E-Utilities_).\nEntrezpy facilitates the implementation of queries to query or download data\nfrom the Entrez databases, e.g. search for specific sequences or publications\nor fetch your favorite genome. For more complex queries ``entrezpy`` offers the\nclass ``entrezpy.conduit.Conduit`` to run query pipelines or cache results.\n\nLicence and Copyright\n---------------------\n\n``entrezpy`` is licensed under the `GNU Lesser General Public License v3\n(LGPLv3)`_ or later. Please see https://www.ncbi.nlm.nih.gov/home/about/policies/\nconcerning the copyright of the material available through E-Utilities.\n\n\nInstallation\n------------\n\n**Entrezpy requires at least Python 3.6 and the Standars Python Library.**\n\nPyPi\n~~~~\nInstall ``entrezpy`` via PyPi and check:\n\n.. code::\n\n $ pip install entrezpy --user\n\nIf you want to incude entrezpy as part of your pipeline, check the documentation\n(https://entrezpy.readthedocs.io/en/master/setup/installation.html#append-to-sys-path)\n\nDocumentation\n-------------\n\nEntrezpy is fully documented using Spinx\n(http://www.sphinx-doc.org/en/stable/). 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