pseudomancer

A command line tool for reconstructing pseudogenes in prokaryotic genomes.

Installation

# Clone the repository
git clone https://github.com/Floto-Lab/pseudomancer.git
cd pseudomancer

# Create conda environment with all dependencies
mamba env create -f environment.yml
mamba activate pseudomancer_env

Requirements: Mamba or Conda package manager

Usage

# Activate environment (if not already active)
mamba activate pseudomancer_env

# Run pipeline
python -m pseudomancer --genus Mycobacterium --genome target_genome.fasta --out_dir results/

Parameters

• --genus: Genus name for downloading reference proteins from NCBI RefSeq
• --genome: Target genome FASTA file to search for pseudogenes
• --out_dir: Output directory for results
• --evalue: E-value threshold (default: 1e-5)

How it works

1. Identifies all open reading frames (ORFs) in the target genome using getorf
2. Downloads all complete, annotated genomes for the specified genus from NCBI RefSeq
3. Extracts and merges protein sequences from all assemblies
4. Clusters proteins at 99% identity using mmseqs2 to create a non-redundant dataset
5. Searches the clustered proteins against your target genome using mmseqs2 (tblastn-like search)
6. Outputs results in tabular format with alignment statistics