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.
In [3]:
# Run cell with Ctrl + Enter
# Import main pycoQC module
from pycoQC.Barcode_split import Barcode_split
# Import helper functions from pycoQC
from pycoQC.common import jhelp, head, ls
In [2]:
jhelp(Barcode_split)
In [4]:
Barcode_split (
summary_file="./data/Guppy-2.2.4-basecall-1D-DNA_sequencing_summary+barcode.txt.gz",
output_unclassified=True,
output_dir="./results/")
In [5]:
Barcode_split (
summary_file="./data/Guppy-basecall-1D-DNA_sequencing_summary.txt.gz",
barcode_file="./data/Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt.gz",
output_dir="./results/")
In [6]:
Barcode_split (
summary_file="./data/Guppy-basecall-1D-DNA_sequencing_summary.txt.gz",
output_dir="./results/")