Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.
In createTHetAExomeInput.py, quote the filename arguments inside each call to os.system to prevent the shell from parsing the space-containing argument as multiple tokens (i.e. garbage).
Alternative solutions not attempted here:
use subprocess & avoid using the shell altogether; or
use pysam & avoid creating the pileup files on disk.
In createTHetAExomeInput.py, quote the filename arguments inside each call to os.system to prevent the shell from parsing the space-containing argument as multiple tokens (i.e. garbage).
Alternative solutions not attempted here:
Also fixed a typo.