add source arg to monitor metadata source and add test accordingly

.github/workflows/main.yml

@@ -121,9 +121,10 @@ jobs:
         ppanggolin metadata -p mybasicpangenome/pangenome.h5 -s db1 -m metadata/metadata_genes.tsv -a genes
         ppanggolin metadata -p mybasicpangenome/pangenome.h5 -s db2 -m metadata/metadata_genomes.tsv -a genomes
         ppanggolin metadata -p mybasicpangenome/pangenome.h5 -s db3 -m metadata/metadata_families.tsv -a families --omit
-        ppanggolin metadata -p mybasicpangenome/pangenome.h5 -s db4 -m metadata/metadata_rgps.tsv -a RGPs 
-        ppanggolin write_pangenome -p mybasicpangenome/pangenome.h5 --output mybasicpangenome -f --gexf --light_gexf --cpu 1
-        ppanggolin rgp_cluster --pangenome mybasicpangenome/pangenome.h5 -o rgp_cluster_with_metadata --graph_formats graphml 
+        ppanggolin metadata -p mybasicpangenome/pangenome.h5 -s db4 -m metadata/metadata_rgps.tsv -a RGPs
+
+        ppanggolin write_pangenome -p mybasicpangenome/pangenome.h5 --output mybasicpangenome -f --gexf --light_gexf --cpu 1 
+        ppanggolin rgp_cluster --pangenome mybasicpangenome/pangenome.h5 -o rgp_cluster_with_metadata --graph_formats graphml
         cd -
     - name: testing config file
       shell: bash -l {0}
@@ -151,6 +152,18 @@ jobs:
         cd testingDataset
         head organisms.gbff.list | cut -f1  > organisms_names.gbff.head.list
 
-        ppanggolin write_genomes  -p myannopang/pangenome.h5 --output flat_genomes_from_file_org -f --anno organisms.gbff.list --gff  --organisms  organisms_names.gbff.head.list
+        ppanggolin write_genomes  -p myannopang/pangenome.h5 --output flat_genomes_from_file_org -f \
+                                  --anno organisms.gbff.list --gff  --organisms  organisms_names.gbff.head.list 
+
+        ppanggolin write_genomes  -p stepbystep/pangenome.h5 --output flat_genomes_from_cmdline_orgs --proksee \
+                                --organisms GCF_006508185.1_ASM650818v1_genomic,GCF_002088315.1_ASM208831v1_genomic 
+        
+        head organisms.fasta.list | cut -f1  > organisms_names.fasta.head.list 
+        # Default separator is a pipe but a pipe is found in a value of metadata db1. That is why we use another separator here. 
+        ppanggolin write_genomes -p mybasicpangenome/pangenome.h5 --output mybasicpangenome/genomes_outputs \
+                                --organisms organisms_names.fasta.head.list \
+                                  -f --gff --add_metadata --metadata_sep § 
 
-        ppanggolin write_genomes  -p stepbystep/pangenome.h5 --output flat_genomes_from_cmdline_orgs --proksee --organisms GCF_006508185.1_ASM650818v1_genomic,GCF_002088315.1_ASM208831v1_genomic
+        # Pipe separatore is found in metadata source db1. if we don't require this source then the writting with pipe is work fine. 
+        ppanggolin write_genomes -p mybasicpangenome/pangenome.h5 --output mybasicpangenome/genomes_outputs_with_metadata \
+                                                                    -f --gff --add_metadata  --metadata_sources db2 db3 db4

ppanggolin/formats/writeFlatGenomes.py

@@ -404,7 +404,8 @@ def get_organism_list(organisms_filt: str, pangenome: Pangenome) -> Set[Organism
 
 def write_flat_genome_files(pangenome: Pangenome, output: Path,
                             table: bool = False, gff: bool = False, proksee: bool = False, compress: bool = False,
-                     disable_bar: bool = False, fasta=None, anno=None, organisms_filt: str ="all", add_metadata=False, metadata_sep="|"):
+                     disable_bar: bool = False, fasta=None, anno=None, organisms_filt: str ="all", 
+                     add_metadata=False, metadata_sep="|", metadata_sources:List[str]=None):
     """
     Main function to write flat files from pangenome
 
@@ -422,6 +423,7 @@ def write_flat_genome_files(pangenome: Pangenome, output: Path,
     :param anno: File containing the list of GBFF/GFF files for each organism
     :param organism_filt: String used to specify which organism to write. if all, all organisms are written.
     :param metadata_sep: The separator used to join multiple metadata values for element with multiple metadata values from the same source.
+    :param metadata_sources: Sources of the metadata to use and write in the outputs. None means all sources are used.
 
     """
 
@@ -441,7 +443,7 @@ def write_flat_genome_files(pangenome: Pangenome, output: Path,
 
     check_pangenome_info(pangenome, need_annotations=needAnnotations, need_families=needFamilies,need_graph=need_graph,
                          need_partitions=needPartitions, need_rgp=needRegions, need_spots=needSpots,
-                         need_modules=needModules, need_metadata=add_metadata,
+                         need_modules=needModules, need_metadata=add_metadata, sources=metadata_sources,
                          disable_bar=disable_bar)
 
 
@@ -535,7 +537,7 @@ def launch(args: argparse.Namespace):
     write_flat_genome_files(pangenome, args.output,
                     table=args.table, gff=args.gff, proksee=args.proksee,
                     compress=args.compress, disable_bar=args.disable_prog_bar, fasta=args.fasta, anno=args.anno,
-                    organisms_filt=args.organisms, add_metadata=args.add_metadata, metadata_sep=args.metadata_sep)
+                    organisms_filt=args.organisms, add_metadata=args.add_metadata, metadata_sep=args.metadata_sep, metadata_sources=args.metadata_sources)
 
 
 def subparser(sub_parser: argparse._SubParsersAction) -> argparse.ArgumentParser:
@@ -587,7 +589,11 @@ def parser_flat(parser: argparse.ArgumentParser):
                         required=False, 
                         action="store_true", 
                         help="Include metadata information in the output files if any have been added to pangenome elements (see ppanggolin metadata command).")
-
+    optional.add_argument("--metadata_sources", 
+                    default=None,
+                    nargs="+",
+                    help="Which source of metadata should be written. By default all metadata sources are included.")
+
     optional.add_argument("--metadata_sep", 
                         required=False, 
                         default='|',