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SV Input

STRUCTURAL VARIANT MATRIX GENERATION

INPUT FORMAT:

First six columns are required, and either the column "svclass" (deletion, translocation, tandem-duplication, or inversion) or the columns "strand1" & "strand2" (BRASS convention) must also be present

Example with SV class present (tsv or csv file):

chrom1 start1 end1 chrom2 start2 end2 svclass
19 21268384 21268385 19 21327858 21327859 deletion

Example without SV class present (tsv or csv file):

chrom1 start1 end1 chrom2 start2 end2 strand1 strand2
19 21268384 21268385 19 21327858 21327859 + +

SV Quick Start Example:

#navigate to SVMatrixGenerator directory and start python3 interpreter

from SigProfilerMatrixGenerator.scripts import SVMatrixGenerator as sv
input_dir = "./SigProfilerMatrixGenerator/references/SV/example_input/560-Breast" #directory which contains collection of bedpe files (one per sample)
output_dir = "./SigProfilerMatrixGenerator/references/SV/"
project = "560-Breast"
sv.generateSVMatrix(input_dir, project, output_dir)
Alternatively, you can run directly from the command line: 
python3 ./SigProfilerMatrixGenerator/scripts/SVMatrixGenerator.py ./SigProfilerMatrixGenerator/references/SV/example_input/560-Breast 560-Breast ./SigProfilerMatrixGenerator/references/SV/example_output/ #provide input_dir, project, output_dir as command-line arguments

Setting up R environment with conda (optional but recommended if using R):

conda create --name spmg_r_1.2.13 -y
conda activate spmg_r_1.2.13
conda install python=3.10 r-base r-devtools r-reticulate -c conda-forge -y
pip install SigProfilerMatrixGenerator
echo 'devtools::install_github("AlexandrovLab/SigProfilerMatrixGeneratorR")' | Rscript -

From within a R session, you can now generate the matrices as follows: 

$ R
>> library("reticulate")
>> use_python("path_to_your_python3")
>> py_config()
>> library("SigProfilerMatrixGeneratorR")

>> sv <- SVMatrixGenerator("[your_repo]/test_data/SV", "test_CNV",  "[your_repo]/test_data/")

Function Arguments

These are the acceptable parameters that can be passed into the function call.

Required:
- project: Project name for this instance of matrix generation.
Type: string
Example: "560-Breast"

  • input_dir: Path to directory containing SV bedpe files, one per sample.
    Type: string
    Example: "./SigProfilerMatrixGenerator/references/SV/example_input/560-Breast/"

  • output_dir: Path to directory for output files. If this directory doesn't exist, a new one will created.
    Type: string
    Example: "./SigProfilerMatrixGenerator/references/SV/example_output/"