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Dedicated library to query and retrieve data from Entrez databases at NCBI

Project description

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Entrezpy README

Synopsis

$ 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.

Installation

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

PyPi

Install entrezpy via PyPi and check:

$ 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

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