FUBAR Analysis Pipeline

A Python script for running FUBAR (Fast Unconstrained Bayesian AppRoximation for inferring selection) analysis on sequence codon alignment files in batch.

Description

This tool processes FASTA codon alignment files in a directory and runs FUBAR analysis using HyPhy. It automatically discovers FASTA files, checks for corresponding Newick tree files, and processes each alignment that hasn't already been analyzed.

Requirements

• Python 3
• HyPhy with FUBAR method installed
• FASTA alignment files
• Corresponding Newick tree files (.nwk extension)

Installation

Installing HyPhy

Using Conda (recommended):

conda install -c bioconda hyphy

Using Homebrew (macOS):

brew install hyphy

From source:

git clone https://github.com/veg/hyphy.git
cd hyphy
cmake .
make

Using apt (Ubuntu/Debian):

sudo apt-get install hyphy

Verify installation:

hyphy --version

Usage

python3 run_FUBAR.py [options]

Options

• -d, --dir: Directory containing input FASTA files (default: current directory)

Examples

Process FASTA files in the current directory:

python3 run_FUBAR.py

Process FASTA files in a specific directory:

python3 run_FUBAR.py -d /path/to/alignments

Input Files

• FASTA files (.fasta extension): Multiple sequence codon alignments
• Newick tree files (.nwk extension): Phylogenetic trees corresponding to each FASTA file

The script expects tree files to have the same name as the FASTA file with .nwk extension added (e.g., alignment.fasta and alignment.fasta.nwk).

Output

• FUBAR results (.FUBAR.json extension): JSON files containing FUBAR analysis results for each processed alignment

Behavior

• Scans the specified directory for all .fasta files
• For each FASTA file, checks if a corresponding .nwk tree file exists
• Skips files that already have .FUBAR.json output files
• Runs FUBAR analysis using HyPhy for files that need processing
• Exits with error if a tree file is missing for any FASTA file

Error Handling

The script will exit with an error message if any FASTA file lacks a corresponding Newick tree file.