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LZGraphs Documentation

API Reference

MuteJester/LZGraphs

API Reference¶

Complete reference documentation for all LZGraphs classes and functions.

Graph Classes¶

AAPLZGraph - Amino acid graphs
NDPLZGraph - Nucleotide graphs
NaiveLZGraph - Non-positional graphs

Analysis¶

Metrics - Diversity and entropy
Utilities - Helper functions
Exceptions - Error handling

Import Patterns¶

Core Classes¶

from LZGraphs import AAPLZGraph, NDPLZGraph, NaiveLZGraph

Metrics Functions¶

from LZGraphs import (
    K1000_Diversity,
    K_Diversity,
    LZCentrality,
    node_entropy,
    edge_entropy,
    graph_entropy,
    jensen_shannon_divergence
)

Utilities¶

from LZGraphs import LZBOW, NodeEdgeSaturationProbe
from LZGraphs.utilities import lempel_ziv_decomposition, generate_kmer_dictionary

Visualization¶

from LZGraphs.visualization import (
    draw_graph,
    ancestors_descendants_curves_plot,
    sequence_possible_paths_plot,
    sequence_genomic_node_variability_plot,
    sequence_genomic_edges_variability_plot
)

Class Hierarchy¶

LZGraphBase (abstract)
├── AAPLZGraph - Amino acid positional
├── NDPLZGraph - Nucleotide double positional
└── NaiveLZGraph - No positional encoding

LZBOW - Bag of Words encoder
NodeEdgeSaturationProbe - Saturation analysis

Exceptions:
LZGraphError (base)
├── InputValidationError
│   ├── EmptyDataError
│   ├── MissingColumnError
│   └── InvalidSequenceError
├── GraphConstructionError
├── GeneDataError
│   ├── NoGeneDataError
│   └── GeneAnnotationError
├── WalkError
│   ├── NoValidPathError
│   └── MissingNodeError
└── ...

Common Methods¶

All graph classes share these methods:

Method	Description
`walk_probability(walk)`	Calculate sequence probability
`random_walk()`	Generate a random sequence
`save(filepath)`	Save graph to disk
`load(filepath)`	Load graph from disk
`encode_sequence(seq)`	Encode sequence to walk
`clean_node(node)`	Extract pattern from node

Version Information¶

import LZGraphs
print(LZGraphs.__version__)

Module Structure¶

LZGraphs/
├── __init__.py           # Main exports
├── graphs/
│   ├── amino_acid_positional.py
│   ├── nucleotide_double_positional.py
│   └── naive.py
├── metrics/
│   ├── diversity.py
│   └── entropy.py
├── utilities/
│   ├── utilities.py
│   └── node_edge_saturation_probe.py
├── bag_of_words/
│   └── bow_encoder.py
├── visualization/
│   └── visualize.py
└── exceptions/
    └── __init__.py