https://github.com/jmaupetit/bio_eutils

Standalone Entrez module from BioPython
https://github.com/jmaupetit/bio_eutils

Last synced: 2 months ago
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Standalone Entrez module from BioPython

• Host: GitHub
• URL: https://github.com/jmaupetit/bio_eutils
• Owner: jmaupetit
• License: other
• Created: 2012-03-14T17:57:25.000Z (almost 13 years ago)
• Default Branch: master
• Last Pushed: 2017-05-18T06:12:09.000Z (over 7 years ago)
• Last Synced: 2024-10-17T03:54:43.429Z (3 months ago)
• Language: Python
• Homepage:
• Size: 986 KB
• Stars: 6
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Bio_Eutils

## Introduction

Bio_Eutils is the standalone version of the Entrez and Medline

[BioPython](http://www.biopython.org) modules. It is used to access to

the [NCBI E-utilities](http://www.ncbi.nlm.nih.gov/books/NBK25501/) -

a set of (web)services to query Entrez databases.

## Version

The latest version of the module follows the latest biopython release:

[1.65](http://biopython.org/wiki/Download) at this time.

## Installation

The main purpose of this module is to keep the installation step as

small and simple as possible. Hence the module comes with no other

dependencies. You can either choose to clone the repository or install

it from pip.

### Clone the module from [Github](git://github.com/jmaupetit/Bio_Eutils.git)

    git clone git://github.com/jmaupetit/Bio_Eutils.git

    cd Bio_Eutils

    python setup.py install

### Install from PyPI with pip

    pip install Bio_Eutils

## Usage

A sample script to fetch references from J. Monod follows.

	

	from Bio_Eutils import Entrez, Medline

    Entrez.email = "[email protected]"

    

	# Search for PMIDs from author text based search

    handle = Entrez.esearch(db="pubmed", retmax=100, term="monod j[author]")

    pub_search = Entrez.read(handle)

    handle.close()

	

    # Fetch matching entries

    handle = Entrez.efetch(db='pubmed', id=pub_search['IdList'], retmax=20, rettype="medline", retmode="text")

    pub_items = Medline.parse(handle)

    

    # Work with it

    for pub_item in pub_items:

	    print "*" * 10

        print "%s - %s." % (

            pub_item.get("TI","?"),

            ", ".join(pub_item.get("AU","?"))

            )

    handle.close()

For more informations about the Entrez and Medline modules, refer to

the

[Biopython documentation](http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc96).

## Running tests

If you want to contribute to this project, you may want to run tests. This could be achieve *via*:

    $ cd Tests

    $ python run_tests.py

## Disclaimer

> Please not that [J. Maupetit](http://julien.maupetit.me) is not the

> author of the Bio.Entrez and Bio.Medline packages. He only maintains

> this standalone version for his own usage. The Bio.* modules are

> distributed under the Biopython license agreement (see LICENSE).