fixed bugs for proteomicslfq

onsite/ascore/cli.py

@@ -204,10 +204,26 @@ def ascore(
                 else:
                     stats["errors"] += 1
 
+        # Count how many PSMs had their modification sites reassigned
+        relocated_count = 0
+        orig_pf_map = {}
+        for _, group_df in grouped:
+            pep_idx = group_df.iloc[0].get("peptide_identification_index")
+            orig_pf = str(group_df.iloc[0].get("peptidoform", ""))
+            if orig_pf:
+                orig_pf_map[pep_idx] = orig_pf
+        for row in result_rows:
+            pep_idx = row.get("peptide_identification_index")
+            orig_pf = orig_pf_map.get(pep_idx, "")
+            out_pf = str(row.get("peptidoform", ""))
+            if orig_pf and orig_pf != out_pf:
+                relocated_count += 1
+
         elapsed = time.time() - start_time
-        click.echo(f"\nProcessing Complete:")
+        click.echo("\nProcessing Complete:")
         click.echo(f"  Total identifications: {stats['total']}")
         click.echo(f"  Successfully processed: {stats['processed']}")
+        click.echo(f"  Modification sites reassigned: {relocated_count}")
         click.echo(f"  Phosphorylated peptides: {stats['phospho']}")
         click.echo(f"  Processing errors: {stats['errors']}")
         click.echo(f"  Time elapsed: {elapsed:.2f} seconds")

onsite/idparquet.py

@@ -265,7 +265,7 @@ def _pa_col(name, values):
         return pa.array(values, type=tbl.schema.field(name).type)
 
     updates = {}
-    for col in ("peptidoform", "sequence", "score", "score_type", "higher_score_better"):
+    for col in ("peptidoform",):
         updates[col] = _pa_col(col, psms_df[col].tolist())
 
     updates["psm_metavalues"] = _pa_col("psm_metavalues", psms_df["psm_metavalues"].tolist())

onsite/lucxor/cli.py

@@ -21,8 +21,7 @@
     MSExperiment,
     SpectrumLookup,
     AASequence, 
-    PeptideHit, 
-    PeptideIdentification
+    PeptideHit
 )
 
 from onsite.idparquet import pyopenms_to_unimod_notation, save_dataframes, load_dataframes, unimod_to_pyopenms_notation
@@ -245,6 +244,7 @@ def lucxor(
             debug=debug,
             add_decoys=add_decoys,
             fragment_method=fragment_method,
+            modeling_score_threshold=modeling_score_threshold,
         )
 
     try:
@@ -747,7 +747,21 @@ def run(
         # 6. Build output DataFrame (using second round calculation results)
 
         result_rows = []
-        phospho_count = 0
+        relocated_count = 0
+
+        # Pre-filter hit_index == 0 rows once, outside the loop
+        _lucxor_df = getattr(self, "_psms_df_template", None)
+        _input_by_ref = {}
+        if _lucxor_df is not None:
+            _hit0 = _lucxor_df[_lucxor_df["hit_index"] == 0]
+            for _, row in _hit0.iterrows():
+                ref = str(row.get("spectrum_reference", ""))
+                if ref:
+                    _input_by_ref[ref] = {
+                        "peptidoform": str(row.get("peptidoform", "")),
+                        "psm_metavalues": row.get("psm_metavalues"),
+                    }
+
         for pep_idx, psm in enumerate(all_psms):
             # Use metadata stashed during load_input_files
             mz = getattr(psm, "_mz", 0.0)
@@ -775,6 +789,20 @@ def run(
 
             peptidoform = pyopenms_to_unimod_notation(seq_str).upper()
 
+            # Build psm_metavalues: preserve original + add Luciphor scores
+            _in_rec = _input_by_ref.get(spec_ref)
+            if _in_rec is not None:
+                _orig_mv = _in_rec["psm_metavalues"]
+                _orig_list = list(_orig_mv) if isinstance(_orig_mv, np.ndarray) else []
+            else:
+                _orig_list = []
+
+            # Track how many peptides had their modification positions changed
+            if _in_rec is not None:
+                orig_peptidoform = _in_rec["peptidoform"]
+                if orig_peptidoform and orig_peptidoform != peptidoform:
+                    relocated_count += 1
+
             # Use pyOpenMS to get unmodified string if possible
             try:
                 seq_obj = AASequence.fromString(seq_str) if seq_str else None
@@ -786,17 +814,6 @@ def run(
                 # Fallback: strip all (...) modification annotations and uppercase
                 base_seq = re.sub(r"\([^)]*\)", "", seq_str).upper()
 
-            # Build psm_metavalues: preserve original + add Luciphor scores
-            _lucxor_df = getattr(self, "_psms_df_template", None)
-            if _lucxor_df is not None:
-                _best = _lucxor_df[_lucxor_df["hit_index"] == 0]
-                if pep_idx < len(_best):
-                    _orig_mv = _best.iloc[pep_idx].get("psm_metavalues")
-                    _orig_list = list(_orig_mv) if isinstance(_orig_mv, np.ndarray) else []
-                else:
-                    _orig_list = []
-            else:
-                _orig_list = []
             _lucxor_managed = {"search_engine_sequence", "Luciphor_pep_score", "Luciphor_global_flr",
                                "Luciphor_local_flr", "Luciphor_site_scores"}
             _filtered_orig = [m for m in _orig_list if isinstance(m, dict) and m.get("name") not in _lucxor_managed]
@@ -844,12 +861,6 @@ def run(
                 "run_identifier": "",
             })
 
-            try:
-                if "(Phospho)" in seq_str:
-                    phospho_count += 1
-            except Exception:
-                pass
-
         # 7. Save results (idParquet format)
         out_df = pd.DataFrame(result_rows) if result_rows else pd.DataFrame()
         save_dataframes(output, out_df, prot_ids, template_df=self._psms_df_template, source_idparquet=input_id)
@@ -864,7 +875,7 @@ def run(
         print("\nProcessing Complete:")
         print(f"  Total identifications: {total}")
         print(f"  Successfully processed: {processed}")
-        print(f"  Phosphorylated peptides: {phospho_count}")
+        print(f"  Relocated: {relocated_count}")
         print(f"  Processing errors: {errors}")
         print(f"  Time elapsed: {elapsed:.2f} seconds")
         if elapsed > 0:
@@ -875,7 +886,7 @@ def run(
             self.logger.info({
                 "total": total,
                 "processed": processed,
-                "phospho": phospho_count,
+                "reassigned": relocated_count,
                 "errors": errors,
                 "elapsed_sec": round(elapsed, 2),
                 "speed_ids_per_sec": round(processed/elapsed, 2) if elapsed > 0 else None

onsite/onsitec.py

@@ -20,7 +20,7 @@
 from onsite.idparquet import load_dataframes, save_dataframes, unimod_to_pyopenms_notation
 
 @click.group()
-@click.version_option(version="0.0.3")
+@click.version_option(version="0.0.4")
 def cli():
     """
     OnSite: Mass spectrometry post-translational modification localization tool
@@ -108,6 +108,13 @@ def cli():
     default=False,
     help="Include A (PhosphoDecoy) as potential phosphorylation site for all algorithms",
 )
+@click.option(
+    "--modeling-score-threshold",
+    "modeling_score_threshold",
+    type=float,
+    default=0.95,
+    help="Score threshold for LucXor model training (default: 0.95, auto-adjusted based on score type)",
+)
 def all(
     in_file,
     id_file,
@@ -118,6 +125,7 @@ def all(
     threads,
     debug,
     add_decoys,
+    modeling_score_threshold,
 ):
     """Run all three algorithms (AScore, PhosphoRS, LucXor) and merge results."""
     try:
@@ -164,17 +172,19 @@ def all(
             click.echo(f"\n{'='*60}")
             click.echo(f"[{time.strftime('%H:%M:%S')}] Running LucXor...")
             click.echo(f"{'='*60}")
-            from onsite.lucxor.cli import lucxor as lucxor_func
+            from onsite.lucxor.cli import PyLuciPHOr2, setup_logging as lucxor_setup_logging
 
             if add_decoys:
                 target_mods = ("Phospho (S)", "Phospho (T)", "Phospho (Y)", "PhosphoDecoy (A)")
             else:
                 target_mods = ("Phospho (S)", "Phospho (T)", "Phospho (Y)")
 
-            ctx = click.Context(lucxor_func)
-            ctx.invoke(
-                lucxor_func,
-                input_spectrum=in_file, input_id=id_file, output=lucxor_out,
+            lucxor_setup_logging(debug, None, lucxor_out)
+            tool = PyLuciPHOr2()
+            tool.run(
+                input_spectrum=in_file,
+                input_id=id_file,
+                output=lucxor_out,
                 fragment_method=fragment_method,
                 fragment_mass_tolerance=fragment_mass_tolerance,
                 fragment_error_units=fragment_mass_unit,
@@ -184,16 +194,18 @@ def all(
                 decoy_mass=79.966331,
                 decoy_neutral_losses=("X -H3PO4 -97.97690",),
                 max_charge_state=5, max_peptide_length=40, max_num_perm=16384,
-                modeling_score_threshold=0.95, scoring_threshold=0.0,
+                modeling_score_threshold=modeling_score_threshold, scoring_threshold=0.0,
                 min_num_psms_model=50, threads=threads, rt_tolerance=0.01,
-                debug=debug, log_file=None, disable_split_by_charge=False,
+                debug=debug, disable_split_by_charge=False,
             )
 
+
+
             # Merge results
             click.echo(f"\n{'='*60}")
             click.echo(f"[{time.strftime('%H:%M:%S')}] Merging results...")
             click.echo(f"{'='*60}")
-            merge_algorithm_results(ascore_out, phosphors_out, lucxor_out, out_file)
+            merge_algorithm_results(ascore_out, phosphors_out, lucxor_out, out_file, id_file)
 
         elapsed = time.time() - start_time
         click.echo(f"\n{'='*60}")
@@ -408,8 +420,24 @@ def merge_algorithm_results(ascore_file, phosphors_file, lucxor_file, output_fil
 
     out_df = full_df.reset_index()
 
+    # Count how many peptides had their modification sites reassigned by LucXor
+    relocated_count = 0
+    input_psms_df, _, _, _ = load_dataframes(input_idparquet)
+    input_pf_map = {}
+    for _, row in input_psms_df.iterrows():
+        pep_idx = row.get("peptide_identification_index")
+        if pep_idx is not None:
+            input_pf_map[pep_idx] = str(row.get("peptidoform", ""))
+    for _, row in out_df.iterrows():
+        pep_idx = row.get("peptide_identification_index")
+        out_pf = str(row.get("peptidoform", ""))
+        orig_pf = input_pf_map.get(pep_idx, "")
+        if orig_pf and orig_pf != out_pf:
+            relocated_count += 1
+
     save_dataframes(output_file, out_df, proteins_df, template_df=lucxor_df, source_idparquet=input_idparquet)
     click.echo(f"Successfully merged {stats['merged']} peptide identifications")
+    click.echo(f"  Modification sites reassigned: {relocated_count}")
     click.echo("Each peptide contains scores from all three algorithms")
 
 
@@ -418,6 +446,7 @@ def run_all_algorithms_from_single_cli(
     fragment_mass_tolerance, fragment_mass_unit,
     threads, debug, add_decoys,
     fragment_method="CID",
+    modeling_score_threshold=0.95,
 ):
     """Run all three algorithms when --compute-all-scores is specified."""
     try:
@@ -470,7 +499,7 @@ def run_all_algorithms_from_single_cli(
                 decoy_mass=79.966331,
                 decoy_neutral_losses=("X -H3PO4 -97.97690",),
                 max_charge_state=5, max_peptide_length=40, max_num_perm=16384,
-                modeling_score_threshold=0.95, scoring_threshold=0.0,
+                modeling_score_threshold=modeling_score_threshold, scoring_threshold=0.0,
                 min_num_psms_model=50, threads=threads, rt_tolerance=0.01,
                 debug=debug, disable_split_by_charge=False,
             )

onsite/phosphors/cli.py

@@ -253,11 +253,27 @@ def phosphors(
                             f"Error processing identification: {res.get('reason', 'unknown')}"
                         )
 
+        # Count how many PSMs had their modification sites reassigned
+        relocated_count = 0
+        orig_pf_map = {}
+        for _, group_df in grouped:
+            pep_idx = group_df.iloc[0].get("peptide_identification_index")
+            orig_pf = str(group_df.iloc[0].get("peptidoform", ""))
+            if orig_pf:
+                orig_pf_map[pep_idx] = orig_pf
+        for row in result_rows:
+            pep_idx = row.get("peptide_identification_index")
+            orig_pf = orig_pf_map.get(pep_idx, "")
+            out_pf = str(row.get("peptidoform", ""))
+            if orig_pf and orig_pf != out_pf:
+                relocated_count += 1
+
         # Report
         elapsed = time.time() - start_time
         click.echo(f"\nProcessing Complete:")
         click.echo(f"  Total identifications: {stats['total']}")
         click.echo(f"  Successfully processed: {stats['processed']}")
+        click.echo(f"  Modification sites reassigned: {relocated_count}")
         click.echo(f"  Phosphorylated peptides: {stats['phospho']}")
         click.echo(f"  Processing errors: {stats['errors']}")
         click.echo(f"  Time elapsed: {elapsed:.2f} seconds")

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyonsite"
-version = "0.0.3"
+version = "0.0.4"
 description = "onsite: mass spectrometry post-translational localization tool"
 authors = [
     {name = "BigBio Stack"}

tests/test_output_validation.py

@@ -57,6 +57,7 @@ def test_output_content_validation(self, idparquet_dir, mzml_file):
                 "--input-id", idparquet_dir,
                 "--output", out,
                 "--target-modifications", "Phospho(S),Phospho(T),Phospho(Y)",
+                "--modeling-score-threshold", "0.3",
             ])
             if r.exit_code != 0:
                 pytest.skip(f"LucXor required but failed: {r.output[:200]}")