add full results flag

Author: adraismawur

config/nplinker.toml

@@ -80,6 +80,10 @@ parameters = "version1_parameters_or_version2_parameters"
 # BiG-SCPAPE v2 also runs a `--mix` analysis by default, so you don't need to set this parameter here.
 # An example value could be: "--mibig-version 3.1 --include-singletons --gcf-cutoffs 0.30"
 
+full_results = false
+# [REQUIRED-UNDER-CONDITIONS] Only required for BiG-SCAPE 2
+# Whether to generate a full set of results instead of only the output database for BiG-SCAPE 2
+
 [gnps]
 # Settings for GNPS.
 

src/nplinker/arranger.py

@@ -319,6 +319,7 @@ def _run_bigscape(self) -> None:
             self.bigscape_running_output_dir,
             self.config.bigscape.parameters,
             version,
+            self.config.bigscape.full_results
         )
 
         if version == "1":

src/nplinker/config.py

@@ -70,6 +70,7 @@ def load_config(config_file: str | PathLike) -> Dynaconf:
     Validator("bigscape.parameters", is_type_of=str),
     Validator("bigscape.cutoff", required=True, is_type_of=str),
     Validator("bigscape.version", required=True, is_type_of=str, is_in=["1", "2"]),
+    Validator("bigscape.full_results", required=True, when=Validator("bigscape.version", eq="2"), is_type_of=bool),
     # GNPS
     Validator("gnps.version", required=True, is_type_of=str, is_in=["1", "2"]),
     # Scoring

src/nplinker/genomics/bigscape/runbigscape.py

@@ -17,6 +17,7 @@ def run_bigscape(
     output_path: str | PathLike,
     extra_params: str,
     version: Literal["1", "2"] = "1",
+    full_results: bool = False
 ) -> bool:
     """Runs BiG-SCAPE to cluster BGCs.
 
@@ -100,10 +101,12 @@ def run_bigscape(
                 "cluster",
                 "--pfam-path",
                 os.path.join(PFAM_PATH, "Pfam-A.hmm"),
-                "--db-only-output",
             ]
         )
 
+        if not full_results:
+            args.append("--db-only-output")
+
     # add input and output paths. these are unchanged
     args.extend(["-i", str(antismash_path), "-o", str(output_path)])