mach2 0.0.4

Migration Analysis of Clonal History 2

MACH2

A mathematical framework for inferring migration histories of metastatic cancer from clone phylogeny and the location of extant clones.

Table of contents

1. Installation
   - Prerequisite
   - Install using pip
2. Usage instruction
   - I/O formats
   - Input
   - Output
   - Usage

1. Installation

Prerequisites

• Python - MACH2 requires Python 3.7 or newer.
• ILP solver - MACH2 requires an ILP solver installed to solve PMH-TR. Currently MACH2 only supports Gurobi optimizer, but we are going to add support for more ILP solvers in the future. MACH2 requires a valid Gurobi installation and license key. The location of Gurobi should be present in LD_LIBRARY_PATH (linux) and DYLD_LIBRARY_PATH (macOS) the license key should be saved in the environment variable GRB_LICENSE_KEY.

Install using pip

MACH2 can easily be installed using pip, the package installer for Python. Open a terminal or command prompt and run the following command:

            $ pip install mach2

If you want to use MACH2 with JupyterLab, you'll need additional dependencies. To install these optional dependencies, you can run the following command:

            $ pip install mach2[jupyter]

Usage Instruction

I/O formats

We describe various formats used by MACH2.

1. Tree file : The tree file contains a list of edges that define the structure of a tree. Each line in the file represents an edge, and the edges should be in the format: vertex1 vertex2. For example:

    1   2
    2   3
    2   4 
    1   3
   

2. Labeling file : The labeling file contains the labels assigned to a set of vertices. Each line in the file corresponds to a vertex and the labels are in the format: leaf label. For example:

    1   A
    2   B
    3   C
   

3. Multi-graph file : Like tree file, the multi-graph file contains a list of edges that define the structure of the multi-graph. Each line in the file represents the set of edges between any pair of vertices vertex1 and vertex2 in the format: vertex1 vertex2 #edges. For example:

    A   B   2
    B   A   1
    A   C   1
   

Additionaly, MACH2 can output files in Graphviz DOT format or JSON format.

Input

MACH2 takes as input two files -

1. Input tree file : Tree file describing the input clone tree.
2. Leaf labeling file : Labeling file describing the leaf labeling of input clone tree.

Output

For each solution, MACH2 can output five types of files.

1. Refined tree file : Tree file describing the output refined tree.
2. Vertex labeling file : Labeling file describing the vertex labeling of the refined tree.
3. Refined tree DOT : Refined tree with vertex labeling in DOT format.
4. Migration graph file : Multi-graph file describing the migration graph.
5. Migration graph DOT : Migration graph in DOT format.

Additionaly MACH2 can return JSON file encoding all the solutions (refined tree with vertex labeling and migration graph). The JSON file can be directly passed to MACH2-viz. The exact format of the JSON file is described here.

MACH2 also prints <primary location> <number of migrations> <number of comigrations> Optimal <running time (in seconds)> on console.

Usage

MACH2 can be run using python.

            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)

An example execution

    $ mach2 data/mcpherson_2016/patient1.tree data/mcpherson_2016/patient1.labeling -c data/mcpherson_2016/coloring.txt