2. Scorpio Inference Module

Scorpio CreateDb User Guide

Introduction

The inference.py module is used to perform inference with the Scorpio model. This guide provides instructions on how to use the inference.py script, including the necessary arguments and example usage.

Script Usage

Arguments

The script accepts the following arguments:

• --db_path (str): Path to the database folder
• --number_hit (int): Number of Hits (default: 1)
• --test_fasta (str): Path to the test FASTA file
• --test_embedding (str): Path to the test embedding file (default: "")
• --output (str): Output folder
• --scorpio_model (str): Path to the Scorpio model (checkpoint)
• --max_len (int): Maximum length of sequence
• --batch_size (int): Batch size
• --cal_kmer_freq (bool): Calculate k-mer frequency (default: False)

Example Command

To run the inference.py module, use the following command:

scorpio inference --db_path "./db_path/" \
             --number_hit 10 \
             --test_fasta "./data/data-amr/test.fasta" \
             --test_embedding "" \
             --output "output_results"