November 2018
Intermediate to advanced
360 pages
9h 36m
English
Content preview from Bioinformatics with Python Cookbook - Second Edition
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
Start your free trial
Getting ready
We will use Biopython, which you installed in Chapter 1, Python and the Surrounding Software Ecology. Biopython provides an interface to Entrez, the data retrieval system made available by NCBI. This recipe is made available in the Chapter02/Accessing_Databases.ipynb Notebook.
You will be accessing a live API from NCBI. Note that the performance of the system may vary during the day. Furthermore, you are expected to be a "good citizen" while using it. You will find some recommendations at http://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Usage_Guidelines_and_Requiremen. Notably, you are required to specify an email address with your query. You should try to avoid large number of requests (100 or more) during peak times (between ...