asymtools2's Introduction

AsymTools2

AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets. Note that currently AsymTools is only compatible with data aligned to hg19.

Installation

Preqs

Install CApy

git clone [email protected]:getzlab/CApy.git
cd CApy
pip install -e .

Then install AsymTools

git clone [email protected]:getzlab/AsymTools2.git
cd AsymTools2
pip install -e .

Example usage

from asymtools.annot import *
from asymtools.plotting import *

# Load and annotate maf file
# An example lung cancer maf can be downloaded from https://gdc.cancer.gov/about-data/publications/luad_2014
m = preprocess_maf('test/AN_TCGA_LUAD_PAIR_capture_freeze_FINAL_230.aggregated.capture.tcga.uuid.curated.somatic.maf')

# Plot asymmetries of mutation counts
twin_bar_txplot(m)
twin_bar_repplot(m)

# Plot with correction of genomic content in mutations/Mb
# Choose 'exome' or 'genome' as appropriate
twin_bar_txplot(m,normalization='exome')
twin_bar_repplot(m,normalization='exome')

# In addition to the matplotlib axes, the plotting functions can also return a dataframe with the plotted values
# The columns summarize for each mutation type the total counts (n1,n2), normalized rates if using (r1,r2), and ratio of complementary mutations (ratio)
ax,res = twin_bar_repplot(m,normalization='exome')
print(res[1].head())


plt.show()

Citation

If you use AsymTools in your work, please cite the original publication:

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair

Haradhvala N.J., Polak P. et al., Cell 2016 Jan 21. doi: 10.1016/j.cell.2015.12.050