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 "?":
- In an output cell with the standard help function:
- Inline with the cursor on the function of interest use
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
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.
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)