Merge pull request #191 from AlexandrovLab/SV-VCF

SV VCF

.gitignore

@@ -20,4 +20,9 @@ SigProfilerMatrixGenerator/references/vcf_files/*_bench/logs/
 SigProfilerMatrixGenerator/references/tests/*/input/
 SigProfilerMatrixGenerator/references/tests/*/logs/
 SigProfilerMatrixGenerator/references/tests/*/output/
-SigProfilerMatrixGenerator/install.log
+SigProfilerMatrixGenerator/install.log
+
+# SV Example Files
+SigProfilerMatrixGenerator/references/SV/example_output/*
+SigProfilerMatrixGenerator/references/SV/example_input/VCF/*.tsv
+SigProfilerMatrixGenerator/references/SV/example_input/VCF/*.bedpe

CHANGELOG.md

@@ -6,6 +6,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.2.28] - 2024-08-06
+
+### Added
+- Added support for processing SV input for VCF versions 4.1, 4.2, and 4.3. The tool now supports both the previous input format (requiring the first six columns and either the "svclass" column or the "strand1" & "strand2" columns) and VCF files.
+
+### Changed
+- Updated the README command line examples to use CLI instead of calling the script directly.
+
 ## [1.2.27] - 2024-07-18
 
 ### Added

README.md

@@ -1,4 +1,4 @@
-[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/s93d5/wiki/home/) [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause) [![Build Status](https://travis-ci.com/AlexandrovLab/SigProfilerMatrixGenerator.svg?branch=master)](https://app.travis-ci.com/AlexandrovLab/SigProfilerMatrixGenerator)
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/s93d5/wiki/home/) [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause) [![Build Status](https://app.travis-ci.com/AlexandrovLab/SigProfilerMatrixGenerator.svg?branch=master)](https://app.travis-ci.com/AlexandrovLab/SigProfilerMatrixGenerator)
 [![Uptime Robot status](https://img.shields.io/uptimerobot/status/m795312784-02766a79f207f67626cef289)](https://stats.uptimerobot.com/jjqW4Ulymx)
 
 # SigProfilerMatrixGenerator
@@ -118,24 +118,45 @@ a DBS, SBS, ID, and TSB folder (there will also be a plots folder if this parame
 
 ### Quick Start Example: ###
 
-```
-#navigate to SVMatrixGenerator directory and start python3 interpreter
-
+```python
 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/"
+output_dir = "./SigProfilerMatrixGenerator/references/SV/example_output/"
 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
+```bash
+SigProfilerMatrixGenerator sv_matrix_generator $input_dir $project $output_dir
 ```
 ## OUTPUT:
 1. Annotated bedpe file - a file with each SV annotated with its type, size bin, and clustered/non-clustered status
 2. Aggregate SV plot - a summary plot showing the average number of events in each channel for the whole cohort of samples
 3. SV Matrix - a 32 X n matrix (where n is the number of samples) that can be used to perform signature decomposition, clustering, etc.
 
+### VCF INPUT FORMAT:
+
+**Note that VCF format (4.1, 4.2 and 4.3) is now supported. If using VCFs, please make sure the files in your input directory end with .vcf. Manta, Delly, Lumpy and GRIDSS are supported and example test files can be found in the [references/SV/](https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/tree/master/SigProfilerMatrixGenerator/references/SV) folder**
+
+### Quick Start Example: ###
+
+```python
+#navigate to SVMatrixGenerator directory and start python3 interpreter
+
+from SigProfilerMatrixGenerator.scripts import SVMatrixGenerator as sv
+input_dir = "./SigProfilerMatrixGenerator/references/SV/example_input/VCF/" #directory which contains collection of VCF files (one per sample)
+output_dir = "./SigProfilerMatrixGenerator/references/SV/example_output/"
+project = "vcf-test" #test manta, delly, lumpy, and gridss vcf files
+sv.generateSVMatrix(input_dir, project, output_dir)
+```
+**Alternatively, you can run directly from the command line:**
+```bash
+input_dir="./SigProfilerMatrixGenerator/references/SV/example_input/VCF/"
+project="vcf-test"
+output_dir="results"
+SigProfilerMatrixGenerator sv_matrix_generator $input_dir $project $output_dir
+```
+
 ## COPY NUMBER MATRIX GENERATION
 
 In order to generate a copy number matrix, provide the an absolute path to a multi-sample segmentation file obtained from one of the following copy number calling tools (if you have individual sample files, please combine them into one file with the first column corresponding to the sample name):
@@ -166,8 +187,8 @@ $ python3
 
 **Alternatively, you can run directly from the command line:**
 
-```
-python ./SigProfilerMatrixGenerator/scripts/CNVMatrixGenerator.py BATTENBERG ./SigProfilerMatrixGenerator/references/CNV/example_input/Battenberg_test.tsv BATTENBERG-TEST ./SigProfilerMatrixGenerator/references/CNV/example_output/
+```bash
+SigProfilerMatrixGenerator cnv_matrix_generator BATTENBERG ./SigProfilerMatrixGenerator/references/CNV/example_input/Battenberg_test.tsv BATTENBERG-TEST ./SigProfilerMatrixGenerator/references/CNV/example_output/
 ```
 
 **SUPPORTED GENOMES**