From ecae33492383559633fee0ba1cced93475ec5d4d Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Wed, 27 Nov 2024 10:47:26 +0100
Subject: [PATCH 1/2] clean unused import

---
 ppanggolin/RGP/genomicIsland.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ppanggolin/RGP/genomicIsland.py b/ppanggolin/RGP/genomicIsland.py
index e7d8918d..33373341 100644
--- a/ppanggolin/RGP/genomicIsland.py
+++ b/ppanggolin/RGP/genomicIsland.py
@@ -4,7 +4,7 @@
 import logging
 import argparse
 from pathlib import Path
-from typing import Set, Iterable, List, Tuple
+from typing import Set, Iterable
 
 # installed libraries
 from tqdm import tqdm

From 0875aad5462bfc9210b0a4572c94a4f70cac4ae6 Mon Sep 17 00:00:00 2001
From: JeanMainguy <jean.mainguy@outlook.fr>
Date: Wed, 27 Nov 2024 10:50:07 +0100
Subject: [PATCH 2/2] add score to RGP table in h5

---
 ppanggolin/formats/readBinaries.py  | 6 ++++++
 ppanggolin/formats/writeBinaries.py | 2 ++
 ppanggolin/region.py                | 2 +-
 3 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/ppanggolin/formats/readBinaries.py b/ppanggolin/formats/readBinaries.py
index 650b4bc7..c2607aa1 100644
--- a/ppanggolin/formats/readBinaries.py
+++ b/ppanggolin/formats/readBinaries.py
@@ -971,7 +971,13 @@ def read_rgp(pangenome: Pangenome, h5f: tables.File, disable_bar: bool = False):
             region = pangenome.get_region(row["RGP"].decode())
         except KeyError:
             region = Region(row["RGP"].decode())
+
+            # starting from v2.2.1 score is part of RGP table in h5.
+            if "score" in row.dtype.names:
+                region.score = row["score"]
+
             pangenome.add_region(region)
+
         gene = pangenome.get_gene(row["gene"].decode())
         region.add(gene)
     pangenome.status["predictedRGP"] = "Loaded"
diff --git a/ppanggolin/formats/writeBinaries.py b/ppanggolin/formats/writeBinaries.py
index 17ba76ab..67dc0463 100644
--- a/ppanggolin/formats/writeBinaries.py
+++ b/ppanggolin/formats/writeBinaries.py
@@ -299,6 +299,7 @@ def rgp_desc(max_rgp_len, max_gene_len):
     return {
         "RGP": tables.StringCol(itemsize=max_rgp_len),
         "gene": tables.StringCol(itemsize=max_gene_len),
+        "score": tables.UInt32Col(),
     }
 
 
@@ -355,6 +356,7 @@ def write_rgp(
         for gene in region.genes:
             rgp_row["RGP"] = region.name
             rgp_row["gene"] = gene.ID
+            rgp_row["score"] = region.score
             rgp_row.append()
     rgp_table.flush()
 
diff --git a/ppanggolin/region.py b/ppanggolin/region.py
index e2589e13..39f90326 100644
--- a/ppanggolin/region.py
+++ b/ppanggolin/region.py
@@ -51,7 +51,7 @@ def __init__(self, name: str):
         super().__init__()
         self._genes_getter = {}
         self.name = name
-        self.score = 0
+        self.score = None
         self._starter = None
         self._stopper = None
         self._coordinates = None