consprot

Delineate bacterial genera quickly and transparently using the Percentage Of Conserved Proteins (POCPu) using a validated nextflow workflow

Usage

consprot run --input <directory of genomes> --output <name of output directory>

consprot will run a nextflow workflow locally and compute POCPu values for all pairwise comparisons (except self-comparisons). This means that adding -resume will reuse cached results and only rerun what changed (e.g., additional genomes):

consprot run --input <directory of genomes> --output <name of output directory> -resume

Input

A directory with genome files (.fa, .fna or .fasta).

Upcoming:

• Protein files if already available and/or to bypass pyrodigal
• List of files to bypass nextflow file search

Output

The specified output directory will contain a pocpu.csv with the following columns:

• query: basename of the genome used in this comparison
• subject: basename of the genome used in this comparison
• pocp: value of legacy POCP [0-100]. Could exceed 100 in case of duplicated genes.
• pocpu: value of POCPu [0-100] using only unique matches.

Note: nextflow workflow produce additional files and directory where it is ran. For instance, the log file of the latest run is .nextflow.log, or the working directory with temporary files is work.

Installation

At the moment, install consprot by cloning the repository and follow the development section.

Upcoming: bioconda

Development

To build consprot safely, work in a separate conda environment and install using the dedicated pip:

mamba create -n consprot-dev python pip
conda activate consprot-dev
python -m pip install -e .
consprot -v