User Guide¶

Description¶

The jpredapi package provides a simple Python interface for submitting and retrieving jobs from JPRED: A Protein Secondary Structure Prediction Server (JPRED).

Installation¶

The jpredapi package runs under Python 2.7 and Python 3.4+. Starting with Python 3.4 pip is included by default. To install system-wide with pip run the following:

Install on Linux, Mac OS X¶

python3 -m pip install jpredapi

Install on Windows¶

py -3 -m pip install jpredapi

Install inside virtualenv¶

For an isolated install, you can run the same inside a virtualenv.

$ virtualenv -p /usr/bin/python3 venv  # create virtual environment, use python3 interpreter

$ source venv/bin/activate             # activate virtual environment

$ python3 -m pip install jpredapi      # install jpredapi as usually

$ deactivate                           # if you are done working in the virtual environment

Dependencies¶

jpredapi depends on several Python libraries, it will install its dependencies automatically, but if you wish to install them manually, then run commands below:

docopt for creating jpredapi command-line interface.
To install docopt run the following:
python3 -m pip install docopt  # On Linux, Mac OS X
py -3 -m pip install docopt    # On Windows
requests for sending HTTP/1.1 requesrs to JPRED server.
To install requests Python library run the following:
python3 -m pip install requests  # On Linux, Mac OS X
py -3 -m pip install requests    # On Windows
retrying for controlling status requests.
To install retrying Python library run the following:
python3 -m pip install retrying  # On Linux, Mac OS X
py -3 -m pip install retrying    # On Windows

Basic usage¶

jpredapi can be used in several ways:

As a library within interactive Python shell or Python script and as a command-line tool to:

Submit JPRED job.

Check status of JPRED job.

Retrieve results of JPRED job.

Note

Read The jpredapi Tutorial to learn more and see code examples on using jpred.