Merge pull request #327 from nzmacalasdair/devel

Fix Issue 320 Key error with panaroo-generate-gffs
gtonkinhill · Feb 18, 2025 · 90b7fb3 · 90b7fb3
2 parents 4dc499e + ce0c622
commit 90b7fb3
Showing 1 changed file with 18 additions and 4 deletions.
diff --git a/panaroo/post_run_gff_output.py b/panaroo/post_run_gff_output.py
@@ -8,7 +8,11 @@
 from Bio import SeqIO
 from Bio.Seq import Seq
 
-from .isvalid import is_valid_folder
+#janky workaround to run this as a script 
+try:
+    from .isvalid import is_valid_folder
+except ImportError as e: 
+    from isvalid import is_valid_folder
 #from .__init__ import __version__
 
 def get_options():
@@ -142,7 +146,10 @@ def process_refound_gene(refound_id, pangenome_id, parsed_gff, refound_seqs,
     strand = refound_seqs[refound_id][3]
 
     #Get additional data required for GFF annotation
-    gene_name = G.nodes[pangenome_id]["annotation"]
+    combined_gene_name = G.nodes[pangenome_id]["annotation"]
+    gene_name = "_".join(combined_gene_name.strip(";").split(";")) 
+    panaroo_name = G.nodes[pangenome_id]["name"]
+
     if G.nodes[pangenome_id]["paralog"] == 1:
         has_paralog = "True"
     else:
@@ -153,6 +160,7 @@ def process_refound_gene(refound_id, pangenome_id, parsed_gff, refound_seqs,
                                "locus_tag="+refound_id,
                                "name="+gene_name,
                                "description="+gene_description,
+                               "panaroo_gene_cluster="+panaroo_name,
                                "inference=panaroo refound gene",
                                "has_pangenome_paralog="+has_paralog])
     gff_line = [scaffold_id, "Panaroo_refound", "candidate_gene", str(start+1), str(stop), ".", 
@@ -195,7 +203,11 @@ def create_new_gffs(isolate_index, parsed_gffs, pp_isolate_genes,
                 else:
                     original_gene_data = original_gene_data[0]
                 #Get various other metadata for gene required for GFF3
-                gene_name = G.nodes[pangenome_gene]["annotation"]
+                combined_gene_name = G.nodes[pangenome_gene]["annotation"]
+                gene_name = "_".join(combined_gene_name.strip(";").split(";"))                
+                panaroo_name = G.nodes[pangenome_gene]["name"]
+
+
                 if gene_name == "":
                     gene_name = "No_name"
                 if G.nodes[pangenome_gene]["paralog"] == 1:
@@ -210,8 +222,10 @@ def create_new_gffs(isolate_index, parsed_gffs, pp_isolate_genes,
                                           "description="+gene_description,
                                           "pangenome_id="+str(pangenome_gene),
                                           "panaroo_ID="+gene,
+                                          "panaroo_gene_cluster="+panaroo_name,
                                           "eC_number="+original_gene_data.get("eC_number", str(None)),
-                                          "prepanaroo_inference="+original_gene_data["inference"],
+                                           "prepanaroo_inference="+original_gene_data.get("inference", 
+                                                                                          "Unknown_inference"),
                                           "has_pangenome_paralog="+has_paralog])
                 new_gene_line = "\t".join([original_gene_data["seqid"], 
                                       "Panaroo",