Pre-release
This release is a pre-release and may not be stable for production use.
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
=======================
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
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
File details
Details for the file bdgenomics.mango.pileup-0.0.2a0.tar.gz.
File metadata
- Download URL: bdgenomics.mango.pileup-0.0.2a0.tar.gz
- Upload date:
- Size: 873.4 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/1.9.1 pkginfo/1.4.1 requests/2.14.2 setuptools/39.1.0 requests-toolbelt/0.8.0 tqdm/4.19.5 CPython/2.7.12
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
b0720db56d0aa4f591f80a3f09029966de288e472e60d0082fba016bd3e9d727
|
|
| MD5 |
bdecaa0dc68ded206b32650c8ae1fc9c
|
|
| BLAKE2b-256 |
d28cd32ee25d51ff29fcf8393c6283fe0e99051bb13f5bd463b045527b7ff45b
|
