Metadata-Version: 2.1
Name: entrezpy
Version: 2.1.3
Summary: Dedicated library to query and retrieve data from Entrez databases at NCBI
Home-page: https://gitlab.com/ncbipy/entrezpy.git
Author: Jan P Buchmann
Author-email: jpb@members.fsf.org
License: LGPL
Keywords: bioinformatics NCBI Entrez
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.6
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Database
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Classifier: Development Status :: 5 - Production/Stable

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  :alt: Documentation Status

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  :alt: PyPI - Python Version

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  :alt: PyPI - License

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  :alt: PyPI

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  :alt: PyPI - Format

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  :alt: PyPI - Status

Entrezpy README
===============

Synopsis
--------

.. code::

  $ pip install entrezpy --user

>>> import entrezpy.conduit
>>> w = entrezpy.conduit.Conduit('myemail')
>>> fetch_influenza = w.new_pipeline()
>>> sid = fetch_influenza.add_search({'db' : 'nucleotide', 'term' : 'H3N2 [organism] AND HA', 'rettype':'count', 'sort' : 'Date Released', 'mindate': 2000, 'maxdate':2019, 'datetype' : 'pdat'})
>>> fid = fetch_influenza.add_fetch({'retmax' : 10, 'retmode' : 'text', 'rettype': 'fasta'}, dependency=sid)
>>> w.run(fetch_influenza)

Entrezpy is a dedicated Python library to interact with NCBI_ Entrez
databases [Entrez2016]_ via the E-Utilities ([Sayers2018]_, E-Utilities_).
Entrezpy facilitates the implementation of queries to query or download data
from the Entrez databases, e.g. search for specific sequences or publications
or fetch your favorite genome. For more complex queries ``entrezpy`` offers the
class ``entrezpy.conduit.Conduit`` to run query pipelines or cache results.

Licence and Copyright
---------------------

``entrezpy`` is licensed under the `GNU Lesser General Public License v3
(LGPLv3)`_ or later. Please see https://www.ncbi.nlm.nih.gov/home/about/policies/
concerning the copyright of the material available through E-Utilities.

Please cite the publication if you use entrezpy.

Installation
------------

**Entrezpy requires at least Python 3.6 and the Standars Python Library.**

PyPi
~~~~
Install ``entrezpy`` via PyPi and check:

.. code::

  $ pip install entrezpy --user

If you want to incude entrezpy as part of your pipeline, check the documentation
(https://entrezpy.readthedocs.io/en/master/setup/installation.html#append-to-sys-path)

Documentation
-------------

Entrezpy is fully documented using Spinx
(http://www.sphinx-doc.org/en/stable/). The manual, usage examples and module
reference can be found here: http://entrezpy.readthedocs.io/

``entrezpy`` has been published in Bioinformatics: https://doi.org/10.1093/bioinformatics/btz385

References
----------

.. .. target-notes::

.. [Entrez2016] https://doi.org/10.1093/nar/gkw1071

.. [Sayers2018] https://www.ncbi.nlm.nih.gov/books/NBK25497

.. _NCBI: http://www.ncbi.nlm.nih.gov/

.. _GNU Lesser General Public License v3 (LGPLv3): https://www.gnu.org/licenses/lgpl-3.0.en.html

.. _E-Utilities: https://dataguide.nlm.nih.gov/eutilities/utilities.html