Source Code

Python source code for METAINFORMANT bioinformatics toolkit.

Structure

src/
 metainformant/ # Main package
 core/ # Shared infrastructure
 dna/ # DNA sequence analysis
 rna/ # RNA-seq workflows
 protein/ # Protein analysis
 gwas/ # GWAS pipeline
 visualization/ # Plotting (70+ types)
 networks/ # Biological networks
 singlecell/ # scRNA-seq
 multiomics/ # Multi-omic integration
 ml/ # Machine learning
 math/ # Population genetics theory
 information/ # Information theory
 life_events/ # Event sequence analysis
 ontology/ # GO analysis
 phenotype/ # Trait analysis
 ecology/ # Community ecology
 epigenome/ # Methylation, ChIP-seq
 simulation/ # Synthetic data
 longread/ # Long-read sequencing
 metagenomics/ # Metagenomic analysis
 pharmacogenomics/ # Pharmacogenomic analysis
 spatial/ # Spatial transcriptomics
 structural_variants/ # Structural variant analysis
 quality/ # QC metrics
 menu/ # Interactive CLI

Usage

# Import modules using the current package layout
from metainformant.core import io
from metainformant.core.io import paths
from metainformant.core.utils import config
from metainformant.dna.sequence import core as dna_core
from metainformant.rna.engine import workflow
from metainformant.visualization import plots

# All operations use real implementations (REAL IMPLEMENTATION policy)

Key Patterns

• Core utilities: Use metainformant.core.io, metainformant.core.utils.config, and metainformant.core.utils.logging
• Output: All results go to output/ directory
• Configuration: YAML configs with environment variable overrides
• Type hints: Python 3.11+ with comprehensive typing

Related

• Module Documentation
• API Reference
• Tests