MACH2 Command Line Usage
Along with the Jupyter Notebook/Python API usage described in the quick start guide, MACH2 can be run in command line in all platforms with Python installed.
Input
To run MACH2 in command line, you will need the following files:
- Input tree file: Tree file describing the input clone tree. This is an edgelist file that follows a tsv format. (Example)
- Leaf labeling file: Labeling file describing the leaf labeling of input clone tree. It is in the form of a two-column csv where the first column is a node id and the second column is an anatomic labeling. (Example)
- (Optional) Coloring file: An integer mapping for anatomical locations. For visualization purposes. (Example)
Usage
usage: mach2 [-h] [-p PRIMARY] [-c COLORMAP] [--log] [-o OUTPUT] [-N NSOLUTIONS] [-C] [-t THREADS] [-s] [-S] clone_tree leaf_labeling
MACH2
positional arguments:
clone_tree Input clone tree
leaf_labeling Input leaf labeling
options:
-h, --help show this help message and exit
-p PRIMARY, --primary PRIMARY
Primary anatomical site
-c COLORMAP, --colormap COLORMAP
Color map file
--log Outputs Gurobi logging
-o OUTPUT, --output OUTPUT
Output folder
-N NSOLUTIONS, --nsolutions NSOLUTIONS
Maximum number of solutions retained
-C, --count_solutions
Only prints the number of solutions (default=False)
-t THREADS, --threads THREADS
Number of threads
-s, --suboptimal Returns suboptimal solutions without duplicates, may be slow (default=False)
-S, --seeding_sites Minimizes the number of seeding sites too (default=False)