outputs: Add gene score (= max transcript score)

Author: lisavader

src/geneml/outputs.py

@@ -34,7 +34,7 @@ def get_end_coordinate(end_value, offset=offset):
         "gene",
         get_start_coordinate(gene.start),
         get_end_coordinate(gene.end),
-        ".",
+        f"{gene.score:.3f}",
         strand,
         ".",
         f"ID={gene_id}",

src/geneml/produce_genes.py

@@ -355,6 +355,7 @@ def assign_transcripts_to_genes(transcripts_by_contig_id: dict[str, list[Transcr
                 end=max(t.end for t in group),
                 strand=group[0].strand,
                 transcripts=tuple(group),
+                score=max(t.score for t in group),
             )
             genes_by_contig[contig_id].append(gene)
 

src/geneml/types.py

@@ -92,6 +92,7 @@ class Gene:
     end: int
     strand: int
     transcripts: tuple[Transcript, ...]
+    score: float
 
     def __post_init__(self):
         if not self.transcripts: