a minimal, scriptable genome browser for python built with anywidget
Here be dragons 🐉
pip install pygvimport pygv
# set the reference genome
pygv.ref("mm10")
# set the locus
pygv.locus("chr17:31,531,100-31,531,259")
# create a browser instance
pygv.browse("fragments.bed", "10x_cov.bw")
That's it. By default, pygv infers the track and data-types by file
extension. If a file format has an index file, it must be specified as
a tuple (remote URLs also work):
pygv.browse(
(
"https://example.com/example.bam", # data file
"https://example.com/example.bam.bai" # index file
)
)You can use track to adjust track properties beyond the defaults:
pygv.browse(
pygv.track("10x_cov.bw", name="10x coverage", autoscale=True),
)Multiple tracks are supported by adding to the browse call:
pygv.browse(
# track 1
(
"https://example.com/example.bam",
"https://example.com/example.bam.bai"
),
# track 2
pygv.track("10x_cov.bw", name="10x coverage", autoscale=True),
# track 3
pygv.track("genes.bed", name="Genes", color="blue"),
)create a virtual environment and and install pygv in editable mode with the optional development dependencies:
python -m venv .venv
source .venv/bin/activate
pip install -e ".[dev]"