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CLI

Most analysis APIs are used from Python (import metainformant...). The metainformant entry point (src/metainformant/__main__.py) exposes a small set of commands today.

Entry: uv run python -m metainformant or uv run metainformant.

Implemented commands

Global flags:

  • --version — print package version
  • --modules — list domain module names
  • --help — usage (default when no arguments)

Subcommands:

uv run metainformant protein taxon-ids --file tests/data/protein/taxon_id_list.txt
uv run metainformant protein comp --fasta data/protein/example.faa
uv run metainformant protein rmsd-ca --pdb-a file1.pdb --pdb-b file2.pdb

uv run metainformant quality batch-detect --data samples.csv --batches batches.txt
uv run metainformant quality batch-detect --data samples.csv --batches batches.txt --alpha 0.01

uv run metainformant rna info
uv run metainformant gwas info
Command Purpose
protein taxon-ids Read and print taxon IDs from a file (Protein Proteomes)
protein comp Amino acid composition per sequence from FASTA
protein rmsd-ca Kabsch RMSD between CA atoms of two PDB files
quality batch-detect Batch-effect report from a numeric matrix (CSV) and per-sample batch labels file
rna info Prints RNA sub-package summary (use Python API for workflows)
gwas info Prints GWAS sub-package summary (use Python API or scripts for full runs)

RNA-seq and GWAS workflows (not via main CLI)

The main metainformant CLI does not implement rna run, rna plan, gwas run, dna fetch, or setup. Use one of:

Python API (see RNA Workflow, GWAS Workflow):

from pathlib import Path
from metainformant.rna.engine.workflow import load_workflow_config, plan_workflow, execute_workflow

config = load_workflow_config(Path("config/amalgkit/amalgkit_pogonomyrmex_barbatus.yaml"))
steps = plan_workflow(config)
result = execute_workflow(config, check=False)

Module entry (amalgkit):

uv run python -m metainformant.rna.amalgkit --help

Script orchestrators (recommended for config-driven runs):

python3 scripts/rna/run_workflow.py --config config/amalgkit/amalgkit_pogonomyrmex_barbatus.yaml

TUI variants: TUI Monitoring Tools below.

Tests

Run the test suite with pytest, not via metainformant:

bash scripts/package/test.sh

See Testing.

sequenceDiagram
  participant U as User
  participant Py as Python_API
  participant Eng as rna_engine_workflow
  participant Am as amalgkit_cli
  U->>Py: load_workflow_config(path)
  U->>Py: plan_workflow(config)
  Py->>Eng: plan_workflow
  Eng-->>Py: list_of_steps
  U->>Py: execute_workflow(config, check=True)
  Py->>Eng: execute_workflow
  Eng->>Am: run_amalgkit(step, params)
  Am-->>Eng: subprocess_results
  Eng-->>Py: WorkflowExecutionResult
Loading

See: RNA Workflow, DNA, GWAS Workflow, Testing.

TUI monitoring tools

Interactive terminal tools (separate from metainformant):

  • scripts/rna/monitor_tui.py — Dashboard for pipeline progress and system metrics (default refresh ~5s).

    python scripts/rna/monitor_tui.py

  • scripts/rna/run_workflow_tui.py — Workflow runner with TUI.

    python scripts/rna/run_workflow_tui.py --config config/amalgkit/amalgkit_pogonomyrmex_barbatus.yaml --threads 5

Directory conventions (RNA output)

output/amalgkit/<species>/
├── work/            # Amalgkit intermediate files (metadata, selected samples, merge outputs)
│   ├── metadata/    # Sample metadata from NCBI (metadata_selected.tsv)
│   ├── getfastq/    # Symlinks to downloaded FASTQ files
│   ├── quant/       # Kallisto quantification results per sample
│   ├── merge/       # Combined abundance matrices
│   └── logs/        # Step-level log files
├── fastq/           # Raw downloaded FASTQ files (ENA .fastq.gz or SRA extracts)
│   └── getfastq/    # Per-sample subdirectories with FASTQ pairs
└── genome/          # Reference genome FASTA + Kallisto index

work/getfastq/ holds symlinks to fastq/getfastq/ where data files live.

Configuration files

  • RNA: config/amalgkit/*.yaml (RNA Workflow)
  • GWAS: config/gwas/*.yaml (GWAS Workflow)
  • Networks: config/networks/networks_template.yaml
  • Multi-omics: config/multiomics/multiomics_template.yaml
  • Single-cell: config/singlecell/singlecell_template.yaml

See Configuration Management for environment overrides.