Merge remote-tracking branch 'origin/dev' into projection

labgem · Sep 19, 2023 · 08a5aae · 08a5aae
2 parents 5c50430 + c2e8ef7
commit 08a5aae
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git a/ppanggolin/formats/writeFlat.py b/ppanggolin/formats/writeFlat.py
@@ -535,7 +535,7 @@ def write_stats(output: Path, soft_core: float = 0.95, dup_margin: float = 0.05,
                         nb_gene_core += 1
             completeness = "NA"
             if len(single_copy_markers) > 0:
-                completeness = round(((org.number_of_families() + len(single_copy_markers)) /
+                completeness = round((len(set(org.families) & single_copy_markers) /
                                       len(single_copy_markers)) * 100, 2)
             outfile.write("\t".join(map(str, [org.name,
                                               org.number_of_families(),

diff --git a/ppanggolin/main.py b/ppanggolin/main.py
@@ -120,7 +120,6 @@ def cmd_line() -> argparse.Namespace:
 
     # First parse args to check that nothing is missing or not expected in cli and throw help when requested
     args = parser.parse_args()
-
     if hasattr(args,  "config"):
         # the two subcommand with no common args does not have config parameter. so we can skip this part for them.
         args = manage_cli_and_config_args(args.subcommand, args.config, SUBCOMMAND_TO_SUBPARSER)