jaffatools 0.5.0

Tools for working with JAFFA fusion gene detection

JaffaTools

A Python toolkit for JAFFA fusion gene detection

Instructions

1. Filter FASTQ files: Filter FASTQ files based on the reads in the BAM file and keep only matching reads.
2. Run JAFFA: Encapsulates the running function of the JAFFA fusion gene detection process.
3. Add NB:Z tags: Extract NB:Z tags from the BAM file and add them to the JAFFA result CSV file.
4. jaffa-viz: Visualize JAFFA results
   1. jaffa-viz circos: Creates Circos plots to visualize fusion genes
   2. jaffa-viz cell-stats: Generates statistics about fusion genes per cell
   3. jaffa-viz class-stats: Creates plots showing the classification of fusion genes

Install

pip install jaffatools

Dependencies

System Requirements

• Python: 3.6 or later
• R: 4.0.0 or later (Required for visualization functions)

Python Dependencies

• NumPy: For numerical operations
• pandas: For data manipulation
• pysam: For parsing and manipulating SAM/BAM file
• subprocess: For executing R scripts (built-in)
• argparse: For command-line interface (built-in)
• os: For file path operations (built-in)

R Package Dependencies

The visualization functions require the following R packages:

• data.table: Fast data manipulation
• ggplot2: Statistical data visualization
• RCircos: Circular visualization of genomic data
• gtools: Various R programming tools
• dplyr: Data manipulation grammar

Installation of R Dependencies

You can install all required R packages with the following R command:

install.packages(c("data.table", "ggplot2", "RCircos", "gtools", "dplyr"))  
if (!requireNamespace("BiocManager", quietly = TRUE))  
    install.packages("BiocManager")  
BiocManager::install("RCircos")