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pycoQC API Usage

pycoQC is a simple class that is initialized with a text summary file generated by ONT Albacore or Guppy.

The instantiated object can be subsequently called with various methods that will generates tables and plots.

There are a few different ways to get help for all the public package functions:

  • In a separate window with the jupyter magic "?": ?pycoQC.channels_activity
  • In an output cell with the standard help function: help (pycoQC.channels_activity)
  • Inline with the cursor on the function of interest use shift + tab

Running pycoQC in Jupyter notebook

If you want to run pycoQC interactively in Jupyter you need to install Jupyter manually. If you installed pycoQC in a virtual environment then install Jupyter in the same virtual environment.

pip3 install notebook

Launch the notebook in a shell terminal

jupyter notebook

If it does not auto-start, open the following URL in you favorite web browser http://localhost:8888/tree

From Jupyter homepage you can navigate to the directory you want to work in and create a new Python3 Notebook.

Imports

For plotly offline plotting

Import pycoQC main class as well as Plotly and enable inline plotting in the current Notebook.

This is the recommended option. This ensures that your all your data are stored inside the notebook.

The limitation is that if generating many plots with large datasets the notebook will become quite heavy and slow.

# Run cell with Ctrl + Enter in Jupyter

# Import main pycoQC module
from pycoQC.pycoQC import pycoQC
from pycoQC.pycoQC_plot import pycoQC_plot

# Import helper functions from pycoQC
from pycoQC.common import jhelp

# Import and setup plotly for offline plotting in Jupyter 
from plotly.offline import init_notebook_mode
init_notebook_mode (connected=False)