Add protein name to the gtf ID.

This will prevent issues stemming from merging of multiple
miniprot runs into one file. This can happen when, e.g., multiple
separate protein fasta files are supplied to GALBA.

scorer2gtf.py

@@ -28,7 +28,8 @@ def loadStopCodons(scorerFile):
             proteinEnd = extractAttribute(row, "proteinEnd")
             if proteinEnd == "1":
                 parent = extractAttribute(row, "Parent")
-                validStops.add(parent)
+                prot = extractAttribute(row, "prot")
+                validStops.add(f'{parent}_{prot}')
     return validStops
 
 
@@ -37,25 +38,27 @@ def convert(scorerFile):
     for row in csv.reader(open(scorerFile), delimiter='\t'):
         if row[2] == "mRNA":
             ID = extractAttribute(row, "ID")
+            prot = extractAttribute(row, "prot")
             row[2] = "transcript"
-            row[8] = f'transcript_id "{ID}"; gene_id "{ID}";'
+            row[8] = f'transcript_id "{ID}_{prot}"; gene_id "{ID}_{prot}";'
 
-            if ID in validStops:
+            if f'{ID}_{prot}' in validStops:
                 if row[6] == '+':
                     row[4] = str(int(row[4]) + 3)
                 else:
                     row[3] = str(int(row[3]) - 3)
 
             gene = row.copy()
             gene[2] = "gene"
-            gene[8] = f'gene_id "{ID}";'
+            gene[8] = f'gene_id "{ID}_{prot}";'
             print("\t".join(gene))
             print("\t".join(row))
         elif row[2] == "CDS":
             score = extractAttribute(row, "eScore")
             parent = extractAttribute(row, "Parent")
+            prot = extractAttribute(row, "prot")
             row[5] = score
-            row[8] = f'transcript_id "{parent}"; gene_id "{parent}";'
+            row[8] = f'transcript_id "{parent}_{prot}"; gene_id "{parent}_{prot}";'
             exon = row.copy()
             exon[2] = "exon"
             exon[7] = "."