Sign In Start Free Trial
Account

Add to playlist

Create a Playlist

Modal Close icon
You need to login to use this feature.
  • Book Overview & Buying Bioinformatics with Python Cookbook
  • Table Of Contents Toc
  • Feedback & Rating feedback
Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

By : Tiago R Antao, Tiago Antao
4.7 (6)
close
close
Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

4.7 (6)
By: Tiago R Antao, Tiago Antao

Overview of this book

If you have intermediate-level knowledge of Python and are well aware of the main research and vocabulary in your bioinformatics topic of interest, this book will help you develop your knowledge further.
Table of Contents (11 chapters)
close
close
10
Index

Accessing molecular-interaction databases with PSIQUIC


PSIQUIC (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml) is a consistent interface to many molecular-interaction databases. It's used inside Cytoscape, which is the object of the next recipe. We take this as an opportunity to learn how to interact with PSIQUIC. In this recipe, we will use its REST interface to check the databases that are available and perform some basic querying. We will revisit this in the Cytoscape recipe. You can find this content in the 07_Other/PSICQUIC.ipynb notebook.

How to do it...

Take a look at the following steps:

  1. First, let's define a convenient REST function as follows:

    from __future__ import print_function
    import requests
    def get_psiquic(service, query, full_url=False, **kwargs):
        kwargs['format'] = kwargs.get('format', 'tab27')
        if full_url:
            req = requests.get('%s%s' % (service, query), params=kwargs)
        else:
            server = \ 'http://www.ebi.ac.uk/Tools/webservices/psicquic...

Unlock full access

Continue reading for free

A Packt free trial gives you instant online access to our library of over 7000 practical eBooks and videos, constantly updated with the latest in tech

Create a Note

Modal Close icon
You need to login to use this feature.
notes
bookmark search playlist font-size

Change the font size

margin-width

Change margin width

day-mode

Change background colour

Close icon Search
Country selected

Close icon Your notes and bookmarks

Delete Bookmark

Modal Close icon
Are you sure you want to delete it?
Cancel
Yes, Delete

Delete Note

Modal Close icon
Are you sure you want to delete it?
Cancel
Yes, Delete

Edit Note

Modal Close icon
Write a note (max 255 characters)
Cancel
Update Note

Confirmation

Modal Close icon
claim successful

Buy this book with your credits?

Modal Close icon
Are you sure you want to buy this book with one of your credits?
Close
YES, BUY