palmsite 0.1.1

PalmSite: RdRP catalytic center predictor

PalmSite — RdRP catalytic center predictor

PalmSite is a simple, fast command-line tool that predicts the RNA-dependent RNA polymerase (RdRP) catalytic center from protein FASTA and outputs GFF3.

Highlights

• One command from FASTA → GFF3: palmsite <fasta ...>
• High precision and recall (internal benchmarks):

Backbone (ESM-C)	Positives vs. Negatives	Positives vs. Rest
6b	0.9998	0.9848
600m	0.9992	0.9687
300m	0.9991	0.9755

• Detects distant homologs (e.g., HSRV RdRP(Urayama et al., 2024)).

Installation

pip install palmsite

Quickstart

# Basic (local 600m is default backbone)
palmsite -o hsrv_rdrp-domain.gff examples/hsrv_proteins.fasta
#or
palmsite examples/hsrv_proteins.fasta > hsrv_rdrp-domain.gff

# Quiet mode (only errors)
palmsite -q examples/sars-cov-2_proteins.fasta

# Raise the reporting threshold (default 0.5)
palmsite -p 0.9 examples/zikavirus_proteins.fasta

# Use 6B (Forge); requires a token
palmsite -b 6b -k <FORGE_TOKEN> examples/turnip-mosaic-virus_proteins.fasta
# or export ESM_FORGE_TOKEN and omit -k

Notes:

• -b/--backbone chooses the embedding model: 300m, 600m (local), or 6b (Forge/cloud).

Command-line usage

Usage: palmsite [OPTIONS] [FASTAS]...

  PalmSite — RdRP catalytic center predictor. Usage: palmsite -p 0.5 [-o
  result.gff] [options] <fasta ...>

Options:
  --version                      Show the version and exit.
  -o, --gff-out TEXT             Write GFF3 to this path; default: stdout if
                                 omitted
  -p, --min-p FLOAT              Minimum probability to include a feature in
                                 GFF  [default: 0.5]
  -b, --backbone [300m|600m|6b]  Embedding backbone & size: '300m' (fast,
                                 local), '600m' (balanced, local), '6b'
                                 (highest quality via ESM Forge; requires
                                 --token or ESM_FORGE_TOKEN).  [default: 600m]
  -m, --model-id TEXT            Hugging Face model repo (default via
                                 PALMSITE_MODEL_ID env or palmsite/<backbone>)
  -d, --device [auto|cpu|cuda]   Device for local ESM-C (ignored for 6B Forge)
                                 [default: auto]
  -k, --token TEXT               Forge token (required for 6B if not set in
                                 ESM_FORGE_TOKEN)
  -t, --tmp-dir TEXT             Optional working directory for temp files
  -q, --quiet                    Reduce non-error logs
  -v, --verbose                  Verbose logs (DEBUG level; overrides -q)
  --keep-tmp                     Keep temporary files (sanitized FASTA &
                                 embeddings.h5) for debugging

About -b/--backbone

• 300m – fast local ESM-C. Good for CPU/GPU prototyping.
• 600m – balanced local ESM-C. Better quality; still lightweight.
• 6b – highest quality via ESM Forge (cloud); requires -k <token> or ESM_FORGE_TOKEN.

What PalmSite does

1. Sanitize & merge FASTA
   Replaces unusual residues with X, drops sequences if too many fixes were needed, and writes one merged FASTA.
2. Embed sequences
   • Launches the embedding engine.
   • Backends:
     • Local ESM-C (300m/600m) via Hugging Face.
     • Forge (6B) via the ESM SDK (ESM3ForgeInferenceClient).
3. Predict → GFF3
   Loads the checkpoint from Hugging Face, computes RdRP probabilities and spans, aggregates per protein, and writes GFF3.

Output

• GFF3 (stdout or -o): one feature per protein (catalytic center span). Attributes include P, sigma, original length, and the chunk used.

Environment variables

• ESM_FORGE_TOKEN — Forge API token for -b 6b (alternative to -k).

Project structure (user-side)

• cli.py — top-level command: sanitize → embed → predict.
• embed_shim.py — launches the embedding engine in a subprocess.
• _embed_impl.py — embedding engine (batching, progress, HDF5 writer, Forge/local backends).
• infer_simple.py — simple driver to produce GFF from embeddings.
• _predict_impl.py — full predictor (model, dataset, collate).
• hf.py — Hugging Face weight resolution.
• sanitize.py — FASTA cleaner/merger.
• __init__.py — version. Current: 0.1.0.

Version

0.1.0