Fix config outputs in workflow commands when set in config file

ppanggolin/formats/writeFlatPangenome.py

@@ -636,22 +636,23 @@ def write_persistent_duplication_statistics(pangenome: Pangenome, output: Path,
     return single_copy_persistent
 
 def write_summaries_in_tsv(summaries: List[Dict[str, Any]], output_file: Path,
-                           dup_margin:float, soft_core:float):
+                           dup_margin:float, soft_core:float, compress:bool = False):
     """
     Writes summaries of organisms stored in a dictionary into a Tab-Separated Values (TSV) file.
 
     :param summaries: A list containing organism summaries.
     :param output_file: The Path specifying the output TSV file location.
     :param soft_core: Soft core threshold used
     :param dup_margin: minimum ratio of organisms in which family must have multiple genes to be considered duplicated
+    :param compress: Compress the file in .gz
     """
     # Flatten the nested dictionaries within the summaries dictionary
     flat_summaries = [flatten_nested_dict(summary_info) for summary_info in summaries]
 
     # Create a DataFrame from the flattened summaries
     df_summary = pd.DataFrame(flat_summaries)
 
-    with open(output_file, "w") as flout:
+    with write_compressed_or_not(output_file, compress) as flout:
         flout.write(f"#soft_core={round(soft_core, 3)}\n")
         flout.write(f"#duplication_margin={round(dup_margin, 3)}\n")
 
@@ -702,7 +703,7 @@ def write_stats(output: Path, soft_core: float = 0.95, dup_margin: float = 0.05,
 
         summaries.append(organism_summary)
 
-    write_summaries_in_tsv(summaries, output_file= output / "genomes_statistics.tsv", dup_margin=dup_margin, soft_core=soft_core)
+    write_summaries_in_tsv(summaries, output_file= output / "genomes_statistics.tsv", dup_margin=dup_margin, soft_core=soft_core, compress=compress)
 
     logging.getLogger("PPanGGOLiN").info("Done writing genome per genome statistics")
 

ppanggolin/projection/projection.py

@@ -330,7 +330,7 @@ def write_projection_results(pangenome: Pangenome, organisms: Set[Organism],
     write_summaries_in_tsv(summaries,
                            output_file=output_file,
                            dup_margin=dup_margin,
-                           soft_core=soft_core)
+                           soft_core=soft_core, compress=compress)
 
 
 def summarize_projected_genome(organism: Organism,

ppanggolin/utils.py

@@ -276,7 +276,7 @@ def read_compressed_or_not(file_or_file_path: Union[Path, BinaryIO, TextIOWrappe
             return file_or_file_path
 
 
-def write_compressed_or_not(file_path: Path, compress: bool = False) -> Union[gzip.GzipFile, TextIO]:
+def write_compressed_or_not(file_path: Path, compress: bool = False) -> Union[gzip.GzipFile, TextIOWrapper]:
     """
     Create a file-like object, compressed or not.
 
@@ -736,14 +736,18 @@ def manage_cli_and_config_args(subcommand: str, config_file: str, subcommand_to_
             # overwrite write and draw default when not specified in config 
             if workflow_step == 'write_pangenome':
                 for out_flag in WRITE_PAN_FLAG_DEFAULT_IN_WF:
-                    setattr(default_step_args, out_flag, True)
+                    if out_flag not in config[workflow_step]:
+                        setattr(default_step_args, out_flag, True)
+
             if workflow_step == 'write_genomes':
                 for out_flag in WRITE_GENOME_FLAG_DEFAULT_IN_WF:
-                    setattr(default_step_args, out_flag, True)
+                    if out_flag not in config[workflow_step]:
+                        setattr(default_step_args, out_flag, True)
 
             if workflow_step == "draw":
                 for out_flag in DRAW_FLAG_DEFAULT_IN_WF:
-                    setattr(default_step_args, out_flag, True)
+                    if out_flag not in config[workflow_step]:
+                        setattr(default_step_args, out_flag, True)
 
             step_args = overwrite_args(default_step_args, config_step_args, cli_args)
 

ppanggolin/workflow/all.py

@@ -209,7 +209,7 @@ def launch_workflow(args: argparse.Namespace, panrgp: bool = True,
 
         start_desc = time.time()
 
-        write_pangenome_arguments = ["csv", "Rtab", "gexf", "light_gexf", "projection", "stats", 'json', "families_tsv"]
+        write_pangenome_arguments = ["gexf", "light_gexf", 'json', "csv", "Rtab", "stats", "partitions", "families_tsv"]
 
         # Check that we don't ask write to output something not computed.
         borders, spots, spot_modules, modules, regions = (False, False, False, False, False)