microfrp

MicroFRP is a Snakemake pipeline for assigning microbial functional roles from SPIRE studies using genome-scale reconstructions, community simulations, and interaction scoring.

It downloads MAGs for a SPIRE item, reconstructs metabolic models with gapseq, simulates communities with MICOM, and derives functional role metrics (exchange tendency, cooperation alignment, provisioning bias, and interaction synergy).

Requirements

• Linux (the Pixi environment is pinned to linux-64)
• Pixi for environment management
• Gurobi and CPLEX licenses available at runtime (required by MICOM/optimization)
• Network access to SPIRE endpoints for study metadata and MAG downloads

Setup

Install the environment:

pixi install

Run commands via Pixi:

pixi run snakemake --cores 24

Configuration

Edit config/config.yaml to target a specific SPIRE study and tune simulation settings:

• item: SPIRE item ID (e.g. Lloyd-Price_2019_HMP2IBD)
• reconstruction_tool: reconstruction backend (carve or gapseq)
• tradeoff: MICOM tradeoff value
• growth_media: CSV defining the growth medium
• gapseq_medium: optional gapseq medium argument (only used when reconstruction_tool is gapseq; empty string uses gapseq defaults)

The default growth medium is config/western_diet_gut.csv.

Running the pipeline

From the repository root:

pixi run snakemake --cores 24

This targets the top-level rule and will:

1. Fetch SPIRE samples/MAGs for the configured item.
2. Reconstruct MAG models with gapseq.
3. Build and simulate community models with MICOM.
4. Compute functional role scores and classifications.

Outputs

Key outputs are written to results/:

• results/combined_scores.tsv: numeric scores for each functional role metric
• results/functional_roles.tsv: combined classifications and functional role vectors

Intermediate artifacts are stored in intermediate_outputs/ and downloaded MAGs in external_data/.

Testing

Run a dry run of the workflow:

pixi run test

License

MIT License. See LICENSE.