fix bug in projection of spot

labgem · Nov 30, 2023 · 08f68e9 · 08f68e9
1 parent 897de65
commit 08f68e9
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Showing 5 changed files with 5 additions and 18,292 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -151,6 +151,9 @@ jobs:
                               --organism_name chlam_A --fasta FASTA/GCF_002776845.1_ASM277684v1_genomic.fna.gz \
                               --spot_graph --graph_formats graphml --fast --keep_tmp -f --add_sequences --gff --proksee --table --add_metadata
 
+        ppanggolin projection --pangenome mybasicpangenome/pangenome.h5  -o projection_from_gff_prodigal \
+                              --organism_name chlam_annotated_with_prodigal --anno GBFF/GCF_003788785.1_ct114V1_genomic_prodigal_annotation.gff.gz \
+                               --gff  --table
 
     - name: testing write_genome_cmds
       shell: bash -l {0}

diff --git a/ppanggolin/projection/projection.py b/ppanggolin/projection/projection.py
@@ -914,8 +914,8 @@ def predict_spots_in_input_organisms(
                                                        graph_formats=graph_formats,
                                                        overlapping_match=overlapping_match, set_size=set_size,
                                                        exact_match=exact_match)
-
-        new_spot_id_counter = max((s.ID for s in input_org_spots)) + 1
+        if len(input_org_spots) > 0:
+            new_spot_id_counter = max((s.ID for s in input_org_spots)) + 1
 
         input_org_to_spots[input_organism] = input_org_spots