Tools to work efficiently with bedgraph files.
- Free software: MIT license
- Documentation: https://bdgtools.readthedocs.io.
Use the package manager pip to install foobar.
pip install bdgtools
Create signal plots of tss+-500 :
bdgplot tss CTCF_treat_pileup.bdg genes.bed --rs 1000
or a V-plot over entire gene bodies:
bdgplot v CTCF_treat_pileup.bdg genes.bed
Create average signal plot over peak regions
bdgplot average CTCF_treat_pileup.bdg CTCF_peaks.narrowPeak
or a heatmap over all peak regions
bdgplot average CTCF_treat_pileup.bdg CTCF_peaks.narrowPeak
Save figure to a png file
bdgplot v CTCF_treat_pileup.bdg CTCF_peaks.narrowPeak -o CTCF_vplot.png
or save figure data to pickle
bdgplot v CTCF_treat_pileup.bdg CTCF_peaks.narrowPeak -od CTCF_vplot_data.pkl
Read bedgraph and bedfile from file and show a vplot:
from bdgtools import read_bedgraph, read_bedfile, VPlot, plot
bedgraph = read_bedgraph("CTCF_treat_pileup.bdg")
regions = read_bedfile("CTCF_peaks.narrowPeak")
max_peak_size = max(np.max(r.ends-r.starts) for r in regions)
plotter = VPlot(figure_width=1000)
df = plotter(bedgraph, regions)
plot(df, plotter, show=True)
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
Please make sure to update tests as appropriate.
This package was created with Cookiecutter_ and the audreyr/cookiecutter-pypackage
_ project template.
- _Cookiecutter: https://github.com/audreyr/cookiecutter
- _
audreyr/cookiecutter-pypackage
: https://github.com/audreyr/cookiecutter-pypackage