bdgenomics.mango.pileup 0.0.2a0

bdgenomics.mango.pileup

bdgenomics.mango.pileup
=======================
bdgenomics.mango.pileup is a Jupyter widget that allows users to view genomic reads, variants and features in a python notebook.
bdgenomics.mango.pileup builds off of `pileup.js <https://github.com/hammerlab/pileup.js>`__.
Installation
============
.. code-block:: bash
pip install bdgenomics.mango.pileup
jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup # can be skipped for notebook version 5.3 and above
Usage
=====
.. code-block:: python
import bdgenomics.mango.pileup as pileup
from bdgenomics.mango.pileup.track import *
import pandas as pd

readsJson = pd.read_json("<path_to_GA4GH_json_file>")
GA4GHAlignmentJson = readsJson.to_json()

# make pileup track
tracks=[Track(viz="pileup", label="My Reads", source=pileup.sources.GA4GHAlignmentJson(GA4GHAlignmentJson))]

# render tracks in widget
reads = pileup.PileupViewer(locus="chr17:1-100", reference="hg19", tracks=tracks)
reads