Add results modeling

Author: dsmutin

pipeline.py

@@ -26,6 +26,7 @@
 from PROBESt.misc import write_stats
 from PROBESt.merge import merge
 from PROBESt.args import arguments_parse
+from PROBESt.modeling import run_modeling
 
 # Functions
 
@@ -191,3 +192,7 @@ def merge_iter(iter: int):
 
 write_stats(stats, args.output)
 print("Done\n\nFinish")
+
+# 7. Modeling ----
+modeling_output = os.path.join(args.output, "modeling_results.tsv")
+run_modeling(args, args.input, args.output + "/output.fa", modeling_output)

src/PROBESt/__init__.py

@@ -11,4 +11,5 @@
 from . import models_registry
 from . import AI
 from . import filtration
-from . import tokenization
+from . import tokenization
+from . import modeling

src/PROBESt/args.py

@@ -204,6 +204,12 @@ def arguments_parse():
                         default="70",
                         help="Probe check template option: Minimum identity percentage. Default is 70.")
 
+    parser.add_argument("--visualize",
+                        required=False,
+                        default=True,
+                        type=bool,
+                        help="Whether to create visualizations for probe-target pairs. Default is True.")
+
     args = parser.parse_args()
 
     # Correct args