Add centrality calculation to the command-line interface

[akikuno]

📋 Description

Description:
Add functionality to compute centrality measures in the command-line tool.

The command should take pairwise_similarity_annotations.jsonl as input and calculate:

• Degree centrality
• Betweenness centrality
• Each score normalized by the number of phenotypes associated with each KO mouse.

Expected output example:

{
  "gene1_symbol": "1110059G10Rik",
  "gene2_symbol": "Cog6",
  "phenotype_shared_annotations": {
    "vertebral transformation": {
      "zygosity": "Homo",
      "life_stage": "Early",
      "sexual_dimorphism": "Male"
    }
  },
  "phenotype_similarity_score": 42,
  "centrality": {
    "degree": 1,
    "betweenness": 0.5,
    "normalized_degree": 0.2,
    "normalized_betweenness": 0.1
  }
}

🔖 TSUMUGI Version

0.5.0

📎 Anything else?

No response