Quick Start Example

Quick Start Example

This section provides a quick start guide for using SigProfilerMatrixGenerator.

Step 1: Start Python

Start a Python terminal session and verify you're running Python 3:

python3

You should see output like:

Python 3.5.2 (v3.5.2:4def2a2901a5, Jun 26 2016, 10:47:25)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

Step 2: Verify Installation

Check if SigProfilerMatrixGenerator is installed:

>>> help("modules")

Look for SigProfilerMatrixGenerator in the list of available modules.

If not installed, follow the instructions on the Installation - Python page.

Step 3: Install Reference Genome

Install your desired reference genome:

>>> from SigProfilerMatrixGenerator import install as genInstall
>>> genInstall.install('GRCh37')

This example installs the human GRCh37 assembly. You can install any of the available genome assemblies.

Note:

• ~3 GB of storage is required per genome
• This step may take some time due to large file sizes

Step 4: Prepare Input Files

Place your VCF files in your desired project folder. We recommend naming it based on your project's name.

Supported input formats:

• VCF (Variant Call Format) - one file per sample
• MAF (Mutation Annotation Format)
• ICGC format
• Simple text files (tab-delimited)

Step 5: Generate Matrices

From within a Python session, generate the matrices:

>>> from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen
>>> matrices = matGen.SigProfilerMatrixGeneratorFunc("test", "GRCh37", "/Users/user/Desktop/test", plot=True)

Parameter Layout

SigProfilerMatrixGeneratorFunc(project, reference_genome, path_to_input_files, plot)

Parameter	Description
project	Your project name (string)
reference_genome	Reference genome to use (e.g., "GRCh37", "GRCh38")
path_to_input_files	Full path to directory containing your input VCF files
plot	Set to True to generate visualization plots

Expected Output

After successful execution, you will find the following in your output directory:

project_name/
├── input/          # Copies of input files
├── logs/           # Log and error files
└── output/
    ├── SBS/        # Single base substitution matrices
    ├── DBS/        # Double base substitution matrices
    ├── ID/         # Insertion/deletion matrices
    ├── TSB/        # Transcriptional strand bias results
    ├── plots/      # Visualization plots (if plot=True)
    └── vcf_files/  # Processed VCF files

Complete Example

# Start Python
python3

# Import the module
>>> from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen

# Generate matrices with plotting enabled
>>> matrices = matGen.SigProfilerMatrixGeneratorFunc(
...     "my_cancer_project",      # project name
...     "GRCh37",                  # reference genome
...     "/path/to/my/vcf/files",  # input directory
...     plot=True                  # generate plots
... )

For all function arguments and their types, see the Using the Tool - SBS, ID, DBS Input section.