The latest version of the module follows the latest biopython release: 1.65 at this time.
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 clone git://github.com/jmaupetit/Bio_Eutils.git cd Bio_Eutils python setup.py install
Install from PyPI with pip
pip install Bio_Eutils
A sample script to fetch references from J. Monod follows.
from Bio_Eutils import Entrez, Medline Entrez.email = "firstname.lastname@example.org" # 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.
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
Please not that J. Maupetit 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).