add modules/manifest.json

modules/manifest.json

@@ -16,31 +16,69 @@
       "n_nodes": 785,
       "dense_md5": "b78d7fe5723d7d0baf02c71115e88190",
       "dense_bytes": 1204328966,
-      "matches_gene_lists_txt": true
-    },
-    "PAH": {
-      "n_edges": 741,
-      "n_nodes": 287,
-      "dense_md5": "cf0399f4331452865bd414ca3d3c0728",
-      "dense_bytes": 1204328966,
-      "matches_gene_lists_txt": true
+      "dense_gz": "modules/Asthma_largest_matrix.csv.gz",
+      "edges": "modules/Asthma_edges.csv"
     },
     "CAD": {
       "n_edges": 1949,
       "n_nodes": 751,
       "dense_md5": "11704578713f3817b037bf504b28960b",
       "dense_bytes": 1204328966,
-      "matches_gene_lists_txt": true
+      "dense_gz": "modules/CAD_largest_matrix.csv.gz",
+      "edges": "modules/CAD_edges.csv"
     },
     "COPD": {
       "n_edges": 806,
       "n_nodes": 352,
       "dense_md5": "f1ca0abf4fc8dc5ae43b0a3e1ef99aa3",
       "dense_bytes": 1204328966,
-      "matches_gene_lists_txt": true
+      "dense_gz": "modules/COPD_largest_matrix.csv.gz",
+      "edges": "modules/COPD_edges.csv"
+    },
+    "Fibrosis": {
+      "n_edges": 2366,
+      "n_nodes": 785,
+      "dense_md5": "b78d7fe5723d7d0baf02c71115e88190",
+      "dense_bytes": 1204328966,
+      "dense_gz": "modules/Fibrosis_largest_matrix.csv.gz",
+      "edges": "modules/Fibrosis_edges.csv"
+    },
+    "HI2023": {
+      "n_edges": 350950,
+      "n_nodes": 17350,
+      "dense_md5": "1d6140efdb58d8c383c799196cee07d1",
+      "dense_bytes": 1204328966,
+      "dense_gz": "modules/HI2023_largest_matrix.csv.gz",
+      "edges": "modules/HI2023_edges.csv"
+    },
+    "Inflammation": {
+      "n_edges": 1711,
+      "n_nodes": 523,
+      "dense_md5": "0452bc09ad328e49146762806d5a5f4f",
+      "dense_bytes": 1204328966,
+      "dense_gz": "modules/Inflammation_largest_matrix.csv.gz",
+      "edges": "modules/Inflammation_edges.csv"
+    },
+    "PAH": {
+      "n_edges": 741,
+      "n_nodes": 287,
+      "dense_md5": "cf0399f4331452865bd414ca3d3c0728",
+      "dense_bytes": 1204328966,
+      "dense_gz": "modules/PAH_largest_matrix.csv.gz",
+      "edges": "modules/PAH_edges.csv"
+    },
+    "Thrombosis": {
+      "n_edges": 566,
+      "n_nodes": 287,
+      "dense_md5": "0b5102922c61568b22ed53cb2a009324",
+      "dense_bytes": 1204328966,
+      "dense_gz": "modules/Thrombosis_largest_matrix.csv.gz",
+      "edges": "modules/Thrombosis_edges.csv"
     }
   },
   "gene_order_file": "modules/gene_order.txt",
   "gene_order_md5": "53580290d9f126208b043da1bdb11a3e",
-  "note": "Same content as disease_modelling/submission/data/modules/gene_lists/<M>.txt in the GitHub repo, which stores the pairs space-separated; COPD.txt carries a trailing '{}' edge-attribute column from nx.write_edgelist."
+  "note": "Same content as disease_modelling/submission/data/modules/gene_lists/<M>.txt in the GitHub repo, which stores the pairs space-separated; COPD.txt carries a trailing '{}' edge-attribute column from nx.write_edgelist.",
+  "warning": "Fibrosis_largest_matrix.csv is byte-identical to Asthma_largest_matrix.csv (md5 b78d7fe5...), so one of the two is a copy of the wrong file. HI2023 is the whole interactome (350,950 edges), not a disease module.",
+  "use": "gunzip <M>_largest_matrix.csv.gz to get the exact file the analysis scripts read; the *_edges.csv are the same content as a sparse edge list."
 }