feat: save filename change and parameter --savealignfiles

Author: Selok

lta/commands/run.py

@@ -35,6 +35,7 @@ def run(args: configargparse.Namespace) -> None:
         args.sample_id,
         args.threshold,
         args.boot_reps,
+        args.savealignfiles
     )
     logger.debug("Running pipeline.")
     pl.run()

lta/helpers/pipeline.py

@@ -54,6 +54,7 @@ class Pipeline:
     sample_id: str
     thresh: float
     n: int
+    save_align_files: bool
 
     def __post_init__(self) -> None:
         """Post-process parameters.
@@ -397,7 +398,8 @@ def _generate_jaccard_distance_summary(self) -> pd.DataFrame:
             frames.append(jaccard)
             levels.update(jaccard.index.names)
         summary = utils.merge_dataframe_by_level(datas=frames, levels=levels)
-        summary.to_csv(self.output / "jaccard" / f"jaccard_similarity.csv")
+        if self.save_align_files:
+            summary.to_csv(self.output / "jaccard" / f"jaccard_similarity.csv")
         return summary
 
     def run(self) -> None:
@@ -470,4 +472,4 @@ def run(self) -> None:
         merged_lipid_classes = utils.sort_columns(
             data=merged_lipid_classes, level="Metrics", pressing=["-"]
         )
-        merged_lipid_classes.to_csv(self.output / "merged_lipid_classes.csv")
+        merged_lipid_classes.to_csv(self.output / "swith_lipid_classes_with_stats.csv")

lta/parser.py

@@ -177,4 +177,11 @@
     help="Location of logfile. May also be 'term' for Std.Out.",
 )
 
+lta_parser.add_argument(
+    "--savealignfiles",
+    default=False, 
+    action='store_true',
+    help="Keep a copy of alignment files.",
+)
+
 lta_parser.set_defaults(func=run)