04 Pangenome Analysis
Jupyter notebook from the Antibiotic Resistance Hotspots in Microbial Pangenomes project.
Phase 4: Pangenome Characterization¶
This notebook analyzes the relationship between pangenome structure and ARG diversity:
- Classify species as open vs. closed pangenomes
- Identify whether ARGs are core, accessory, or unique genes
- Correlate pangenome openness with ARG diversity
In [ ]:
import pandas as pd
import numpy as np
from scipy import stats
import matplotlib.pyplot as plt
print("Phase 4: Pangenome Characterization")
Classify Genes by Presence Pattern¶
In [ ]:
# TODO: For each orthogroup, calculate:
# - Core: present in ≥95% of genomes in species
# - Accessory: present in <95% but >0% of genomes
# - Unique: present in only 1 genome
print("Gene classification in progress...")
Assess Pangenome Openness¶
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# TODO: Calculate pangenome openness metrics:
# - Core genes percentage
# - Accessory genes percentage
# - Heap's law parameters (estimates of pangenome growth)
# - Openness scores (higher = more open)
print("Pangenome openness assessment in progress...")
Correlate ARG Categories with Pangenome Openness¶
In [ ]:
# TODO: Test if ARGs are preferentially core, accessory, or unique
# Hypothesis: Open pangenomes may accumulate more accessory ARGs
print("ARG/pangenome correlation analysis in progress...")