basic api runs with all parameters

krishnanlab · Mar 12, 2024 · 6fd8e2d · 6fd8e2d
1 parent d329dd1
commit 6fd8e2d
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Showing 10 changed files with 276 additions and 236 deletions.
diff --git a/example/example_run.py b/example/example_run.py
@@ -40,13 +40,22 @@
     datadir,
     tasks="All",
     networks="STRING",
-    features="Embedding",
-    gscs=["GO", "DisGeNet"],
+    features="SixSpeciesN2V",
+    sp_trn = "Human",
+    sp_tst = "Mouse",
+    gsc= "GO",
 )
 
 # Run through the pipeline
 # First initialize the geneplexus object
-myclass = geneplexus.GenePlexus(datadir, "STRING", "Embedding", "DisGeNet")
+myclass = geneplexus.GenePlexus(
+    file_loc = fp_data,
+    gsc = "Combined",
+    features = "SixSpeciesN2V",
+    net_type = "STRING",
+    sp_trn = "Human",
+    sp_tst = "Mouse",
+)
 
 # Load the input genes into the class and set up positives/negatives
 myclass.load_genes(input_genes)

diff --git a/example/test_download.py b/example/test_download.py
@@ -18,7 +18,7 @@
 )
 parser.add_argument(
     "-data_loc",
-    default="Azure",
+    default="Zenodo",
     type=str,
     help="Where the data is stored (Azure or Zenodo)",
 )

diff --git a/example/test_download_slurm.py b/example/test_download_slurm.py
@@ -9,7 +9,7 @@
 
 tic = time.time()
 
-myloc = "Azure"
+myloc = "Zenodo"
 myamount = "full"
 num_runs = 5
 

diff --git a/geneplexus/_config/config.py b/geneplexus/_config/config.py
@@ -24,9 +24,9 @@
 LOG_LEVELS = ["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"]
 
 ALL_TASKS = ["IDconversion", "MachineLearning", "Similarities", "NetworkGraph", "OriginalGSCs"]
-ALL_NETWORKS = ["BioGRID", "STRING", "STRING-EXP", "GIANT-TN"]
-ALL_FEATURES = ["Adjacency", "Embedding", "Influence"]
-ALL_GSCS = ["GO", "DisGeNet"]
+ALL_NETWORKS = ["BioGRID", "STRING", "IMP"]
+ALL_FEATURES = ["SixSpeciesN2V"]
+ALL_GSCS = ["GO", "Monarch", "DisGeNet", "Combined"]
 ALL_SPECIES = ["Human", "Mouse", "Fly", "Worm", "Fish", "Yeast"]
 
 DEFAULT_LOGREG_KWARGS: Dict[str, Any] = {
@@ -44,16 +44,16 @@
     ("ENSG", "Entrez"),
     ("ENSP", "Entrez"),
     ("ENST", "Entrez"),
+    ("Symbol", "Entrez"),
     ("Entrez", "ENSG"),
     ("Entrez", "Name"),
     ("Entrez", "Symbol"),
-    ("Symbol", "Entrez"),
 }
 
 TASK_TYPE = Literal["IDconversion", "MachineLearning", "Similarities", "NetworkGraph", "OriginalGSCs"]
-NET_TYPE = Literal["BioGRID", "STRING", "STRING-EXP", "GIANT-TN"]
-FEATURE_TYPE = Literal["Adjacency", "Embedding", "Influence"]
-GSC_TYPE = Literal["GO", "DisGeNet"]
+NET_TYPE = Literal["BioGRID", "STRING", "IMP"]
+FEATURE_TYPE = Literal["SixSpeciesN2V"]
+GSC_TYPE = Literal["GO", "Monarch", "DisGeNet", "Combined"]
 SPECIES_TYPE = Literal["Human", "Mouse", "Fly", "Worm", "Fish", "Yeast"]
 
 TASK_SELECTION_TYPE = Union[Literal["All"], TASK_TYPE, List[TASK_TYPE]]