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Using Python Package

You can use a Chromoscope Python package to visualize your local SV files directly on computational notebooks, such as Jupyter Notebook, Jupyter Lab, and Google Colab.

Installation​

You can install the Python package using pip on your terminal.

pip install chromoscope

Open Jupyter Lab​

jupyter lab

We here use Jupyter Lab as an example, but you can also use Jupyter Notebook or Goolge Colab.

Setup Data Config​

In the Data Config, you can specify either a URL to a remote file or a path to the local file on your computer.

!wget https://somatic-browser-test.s3.amazonaws.com/SVTYPE_SV_test_tumor_normal_with_panel.bedpe

config = [{
    "id": "SRR7890905",
    "cancer": "breast",
    "assembly": "hg38",
    "sv": "./SVTYPE_SV_test_tumor_normal_with_panel.bedpe", # path to a local file
    "cnv": "https://gist.githubusercontent.com/sehilyi/6fbceae35756b13472332d6b81b10803/raw/596428a8b0ebc00e7f8cbc52b050db0fbd6e19a5/SRR7890943.ascat.v3.cnv.tsv" # URL to a remote file
}]

Visualize​

Using the data config, you can display Chromoscope visualization.

from chromoscope import Viewer

Viewer.from_config(config)
Python Packae
Figure. Using a Chromoscope Python package on Jupyter Lab

Resource​