Quick Start#

Run MirMachine in a clean working directory. It writes intermediate files under data/ and analyses/ and final outputs under results/predictions/.

Example 1: Standard Node-Based Run#

MirMachine.py -n Caenorhabditis -s Caenorhabditis_elegans \\
             --genome sample/genomes/ce11.fa \\
             --model proto --cpu 20

This searches families associated with the Caenorhabditis node using the proto model set.

Example 2: Restrict to a Single Node Only#

MirMachine.py --node Caenorhabditis --species ce11_single_node \\
             --genome sample/genomes/ce11.fa --single-node-only

Use this when you do not want ancestor/descendant node expansion.

Example 3: Single-Family Run#

MirMachine.py --species ce11_let7 --genome sample/genomes/ce11.fa \\
             --family Let-7 --model combined

This bypasses node selection and searches only the given miRNA family.

Discover Available Inputs#

List valid nodes:

MirMachine.py --print-all-nodes

List available families by model:

MirMachine.py --print-all-families

Show families linked to a specific node:

MirMachine.py --node Caenorhabditis

What Gets Created#

For species name Caenorhabditis_elegans, MirMachine creates:

  • data/yamls/Caenorhabditis_elegans.yaml (run config)

  • results/predictions/gff/Caenorhabditis_elegans.PRE.gff

  • results/predictions/filtered_gff/Caenorhabditis_elegans.PRE.gff

  • results/predictions/fasta/Caenorhabditis_elegans.PRE.fasta

  • results/predictions/heatmap/Caenorhabditis_elegans.heatmap.csv