add metadata to proksee and add test accordingly

labgem · Nov 9, 2023 · 7020706 · 7020706
1 parent 28bc752
commit 7020706
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Showing 4 changed files with 28 additions and 15 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -122,6 +122,10 @@ jobs:
         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 metadata -p mybasicpangenome/pangenome.h5 -s db5 -m metadata/metadata_contigs.tsv  -a contigs
+        ppanggolin metadata -p mybasicpangenome/pangenome.h5 -s db6 -m metadata/metadata_modules.tsv  -a modules
+
+
 
         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
@@ -165,5 +169,6 @@ jobs:
                                   -f --gff --add_metadata --metadata_sep § 
 
         # 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 write_genomes -p mybasicpangenome/pangenome.h5 --output mybasicpangenome/genomes_outputs_with_metadata -f --gff --proksee --add_metadata  --metadata_sources db2 db3 db4
+
+
diff --git a/ppanggolin/formats/write_proksee.py b/ppanggolin/formats/write_proksee.py
@@ -15,7 +15,6 @@
 # local libraries
 from ppanggolin.genome import Organism, Gene
 from ppanggolin.region import Module, Region
-from ppanggolin.pangenome import Pangenome
 
 
 
@@ -100,12 +99,12 @@ def write_tracks(features: List[str]):
     return tracks
 
 
-def initiate_proksee_data(features: List[str], org_name: str, module_to_color: Dict[Module, str]):
+def initiate_proksee_data(features: List[str], organism: Organism, module_to_color: Dict[Module, str]):
     """
     Initializes ProkSee data structure with legends, tracks, and captions.
 
     :param features: A list of features to include in the ProkSee data.
-    :param org_name: The name of the organism for which the ProkSee data is being generated.
+    :param organism: The organism for which the ProkSee data is being generated.
     :param module_to_color: A dictionary mapping modules to their assigned colors.
 
     :return: ProkSee data structure containing legends, tracks, and captions.
@@ -114,7 +113,7 @@ def initiate_proksee_data(features: List[str], org_name: str, module_to_color: D
     proksee_tracks = write_tracks(features)
 
     proksee_captions = {
-        "name": f"{org_name} annotated with PPanGGOLiN",
+        "name": f"{organism.name} annotated with PPanGGOLiN",
         "position": "bottom-center",
         "font": "sans-serif,plain,18",
         "backgroundColor": "rgba(255,255,255,0.4)"
@@ -128,6 +127,7 @@ def initiate_proksee_data(features: List[str], org_name: str, module_to_color: D
         "tracks": proksee_tracks,
         "sequence": {},
         'captions': [proksee_captions],
+        "meta":organism.formatted_metadata_dict() # metadata
     }
 
     return {"cgview": cgview_data}
@@ -149,6 +149,7 @@ def write_contig(organism: Organism, genome_sequences: Dict[str, str] = None) ->
             "name": contig.name,
             "length": contig.length,
             "orientation": "+",
+            "meta":contig.formatted_metadata_dict()
         }
 
         if genome_sequences:
@@ -176,8 +177,10 @@ def write_genes(organism: Organism, disable_bar: bool = True) -> Tuple[List[Dict
     for gene in tqdm(organism.genes, total=organism.number_of_genes(), unit="genes", disable=disable_bar):
         gf = gene.family
         gf2gene[gf.name].append(gene)
-
-        genes_data_list.append({
+
+        metadata_for_proksee  = {f"gene_{k}":v for k, v in gene.formatted_metadata_dict().items()}
+        metadata_for_proksee.update({f"family_{k}":v for k, v in gene.family.formatted_metadata_dict().items()})
+        genes_data_list.append({    
             "name": gene.name,
             "type": "Gene",
             "contig": gene.contig.name,
@@ -188,7 +191,7 @@ def write_genes(organism: Organism, disable_bar: bool = True) -> Tuple[List[Dict
             "tags": [gene.family.named_partition, gene.family.name],
             "source": "Gene",
             "legend": gene.family.named_partition,
-            "meta": ""  # annotations
+            "meta": metadata_for_proksee
         })
 
     # Process RNA genes
@@ -204,7 +207,7 @@ def write_genes(organism: Organism, disable_bar: bool = True) -> Tuple[List[Dict
             "tags": [],
             "source": "Gene",
             "legend": "RNA",
-            "meta": ""  # annotations
+            "meta":  gene.formatted_metadata_dict()
         })
 
     return genes_data_list, gf2gene
@@ -237,7 +240,8 @@ def write_rgp(rgps: Region, organism: Organism, rgp_to_spot_id:Dict[Region,int]=
                 "stop": rgp.stop,
                 "legend": "RGP",
                 "source": "RGP",
-                "tags": tags
+                "tags": tags,
+                "meta": rgp.formatted_metadata_dict()
             })
 
     return rgp_data_list
@@ -275,9 +279,7 @@ def write_modules(modules: List[Module], organism: Organism, gf2genes: Dict[str,
                         "legend": f"module_{module.ID}",
                         "source": "Module",
                         "tags": [f'{completion}% complete'],
-                        "meta": {
-                            "completion": f"{completion}%"
-                        }
+                        "meta": module.formatted_metadata_dict()
                     })
 
     return modules_data_list
@@ -301,7 +303,7 @@ def write_proksee_organism(organism: Organism, output_file: Path,
     This function writes ProkSee data for a given organism, including contig information, genes colored by partition, RGPs,
     and modules. The resulting data is saved as a JSON file in the specified output file.
     """
-    proksee_data = initiate_proksee_data(features, organism.name, module_to_colors)
+    proksee_data = initiate_proksee_data(features, organism, module_to_colors)
 
     proksee_data["cgview"]["sequence"]["contigs"] = write_contig(organism, genome_sequences)
 

diff --git a/testingDataset/metadata/metadata_contigs.tsv b/testingDataset/metadata/metadata_contigs.tsv
@@ -0,0 +1,2 @@
+contigs	Note
+NZ_CP017732.1	Circular  Chromosome 
diff --git a/testingDataset/metadata/metadata_modules.tsv b/testingDataset/metadata/metadata_modules.tsv
@@ -0,0 +1,4 @@
+modules	featureC	featureD	scoreE
+module_0	0	mz_1	.1
+module_1	30	mz_12	.3
+module_2	10	mz_899	.1
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		contigs Note
		NZ_CP017732.1 Circular Chromosome