masster 0.2.0__tar.gz → 0.2.2__tar.gz

{masster-0.2.0 → masster-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.2.0
+Version: 0.2.2
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -730,10 +730,12 @@ Description-Content-Type: text/markdown
 
 # MASSter
 
-**MASSter** is a comprehensive Python package for mass spectrometry data analysis, designed for metabolomics and LC-MS data processing. It provides tools for feature detection, alignment, consensus building, and interactive visualization of mass spectrometry datasets.
+**MASSter** is a comprehensive Python package for mass spectrometry data analysis, designed for metabolomics and LC-MS data processing. It provides tools for feature detection, alignment, consensus building, and interactive visualization of mass spectrometry datasets. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. 
 
 Most core processing functions are derived from OpenMS. We use the same nomenclature and refer to their documentation for an explanation of the parameters. To a large extent, however, you should be able to use the defaults (=no parameters) when calling processing steps.
 
+This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. Novel functionalities will be added based on need and requests.
+
 ## Features
 
 - **Mass spectrometry data processing**: Support for multiple file formats (.wiff, .mzML, .raw, .mzpkl)
@@ -751,7 +753,7 @@ pip install masster
 
 ## Quick Start
 
-### Basic Workflow
+### Basic Workflow for analyzing LC-MS study with 2-... samples
 
 ```python
 import masster
@@ -769,21 +771,33 @@ study.align(rt_max_diff=2.0)
 study.find_consensus(min_samples=3)
 
 # Retrieve missing data for quantification
-study.fill_chrom_parallel()
+study.fill_chrom(abs_)
 
 # Integrate according to consensus metadata
 study.integrate_chrom()
 
-# link MS2 across the whole study
+# link MS2 across the whole study and export them
 study.find_ms2()
-
-# Export MGF file
 study.export_mgf()
 
-# Save the study
+# Save the study to .study5
 study.save()
 ```
 
+### Study-Level Plots
+
+```python
+# Plot features from multiple samples
+study.plot_samples_2d()
+
+# Plot consensus features
+study.plot_consensus_2d()
+
+# Plot overlaid chromatograms for specific consensus features (use their uid)
+study.plot_chrom(uids=[1, 2, 3])
+```
+
+
 ### Single Sample Processing
 
 ```python
@@ -801,15 +815,13 @@ sample.find_adducts()
 # Find MS2 spectra
 sample.find_ms2()
 
-# Save results
+# Save results to .sample5
 sample.save()
 ```
 
-## Visualization Examples
-
 Masster provides extensive plotting capabilities for data exploration and quality control:
 
-### 2D Data Visualization
+### Single sample visualization
 
 ```python
 # Plot 2D overview of MS data with detected features
@@ -822,35 +834,14 @@ sample.plot_2d(
 
 # Plot with feature filtering
 sample.plot_2d(
-    filename="features_ms2_only.html",
-    show_only_features_with_ms2=True,
-    markersize=8
+    filename="features_ms2_only.html"
 )
-```
 
-### Study-Level Plots
-
-```python
-# Plot features from multiple samples
-study.plot_samples_2d(
-    samples=None,  # Use all samples
-    filename="multi_sample_overview.html",
-    markersize=3,
-    alpha_max=0.8
-)
-
-# Plot consensus features
-study.plot_consensus_2d(
-    filename="consensus_features.html",
-    colorby="number_samples",
-    sizeby="inty_mean"
-)
-
-# Plot chromatograms for specific features
-study.plot_chrom(
-    uids=[1, 2, 3],  # Feature UIDs
-    filename="chromatograms.html",
-    aligned=True
+# Plot extracted ion chromatogram
+sample.plot_eic(
+    feature_uid=123,
+    rt_tol=10,
+    mz_tol=0.005
 )
 ```
 
@@ -883,14 +874,6 @@ sample.plot_ms2_cycle(
     filename="ms2_cycle.html",
     centroid=True
 )
-
-# Plot extracted ion chromatogram
-sample.plot_eic(
-    feature_uid=123,
-    rt_tol=10,
-    mz_tol=0.005,
-    filename="eic.html"
-)
 ```
 
 ## File Format Support
@@ -919,13 +902,6 @@ python -m masster.demo.example_batch_process input_directory --recursive --dest
 
 GNU Affero General Public License v3
 
-## Contributing
-
-Contributions are welcome! Please see our contributing guidelines and code of conduct.
-
 ## Citation
 
-If you use Masster in your research, please cite:
-```
-[Citation details to be added]
-```
+If you use Masster in your research, please cite this repository.

{masster-0.2.0 → masster-0.2.2}/README.md

@@ -1,9 +1,11 @@
 # MASSter
 
-**MASSter** is a comprehensive Python package for mass spectrometry data analysis, designed for metabolomics and LC-MS data processing. It provides tools for feature detection, alignment, consensus building, and interactive visualization of mass spectrometry datasets.
+**MASSter** is a comprehensive Python package for mass spectrometry data analysis, designed for metabolomics and LC-MS data processing. It provides tools for feature detection, alignment, consensus building, and interactive visualization of mass spectrometry datasets. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. 
 
 Most core processing functions are derived from OpenMS. We use the same nomenclature and refer to their documentation for an explanation of the parameters. To a large extent, however, you should be able to use the defaults (=no parameters) when calling processing steps.
 
+This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. Novel functionalities will be added based on need and requests.
+
 ## Features
 
 - **Mass spectrometry data processing**: Support for multiple file formats (.wiff, .mzML, .raw, .mzpkl)
@@ -21,7 +23,7 @@ pip install masster
 
 ## Quick Start
 
-### Basic Workflow
+### Basic Workflow for analyzing LC-MS study with 2-... samples
 
 ```python
 import masster
@@ -39,21 +41,33 @@ study.align(rt_max_diff=2.0)
 study.find_consensus(min_samples=3)
 
 # Retrieve missing data for quantification
-study.fill_chrom_parallel()
+study.fill_chrom(abs_)
 
 # Integrate according to consensus metadata
 study.integrate_chrom()
 
-# link MS2 across the whole study
+# link MS2 across the whole study and export them
 study.find_ms2()
-
-# Export MGF file
 study.export_mgf()
 
-# Save the study
+# Save the study to .study5
 study.save()
 ```
 
+### Study-Level Plots
+
+```python
+# Plot features from multiple samples
+study.plot_samples_2d()
+
+# Plot consensus features
+study.plot_consensus_2d()
+
+# Plot overlaid chromatograms for specific consensus features (use their uid)
+study.plot_chrom(uids=[1, 2, 3])
+```
+
+
 ### Single Sample Processing
 
 ```python
@@ -71,15 +85,13 @@ sample.find_adducts()
 # Find MS2 spectra
 sample.find_ms2()
 
-# Save results
+# Save results to .sample5
 sample.save()
 ```
 
-## Visualization Examples
-
 Masster provides extensive plotting capabilities for data exploration and quality control:
 
-### 2D Data Visualization
+### Single sample visualization
 
 ```python
 # Plot 2D overview of MS data with detected features
@@ -92,35 +104,14 @@ sample.plot_2d(
 
 # Plot with feature filtering
 sample.plot_2d(
-    filename="features_ms2_only.html",
-    show_only_features_with_ms2=True,
-    markersize=8
+    filename="features_ms2_only.html"
 )
-```
 
-### Study-Level Plots
-
-```python
-# Plot features from multiple samples
-study.plot_samples_2d(
-    samples=None,  # Use all samples
-    filename="multi_sample_overview.html",
-    markersize=3,
-    alpha_max=0.8
-)
-
-# Plot consensus features
-study.plot_consensus_2d(
-    filename="consensus_features.html",
-    colorby="number_samples",
-    sizeby="inty_mean"
-)
-
-# Plot chromatograms for specific features
-study.plot_chrom(
-    uids=[1, 2, 3],  # Feature UIDs
-    filename="chromatograms.html",
-    aligned=True
+# Plot extracted ion chromatogram
+sample.plot_eic(
+    feature_uid=123,
+    rt_tol=10,
+    mz_tol=0.005
 )
 ```
 
@@ -153,14 +144,6 @@ sample.plot_ms2_cycle(
     filename="ms2_cycle.html",
     centroid=True
 )
-
-# Plot extracted ion chromatogram
-sample.plot_eic(
-    feature_uid=123,
-    rt_tol=10,
-    mz_tol=0.005,
-    filename="eic.html"
-)
 ```
 
 ## File Format Support
@@ -189,13 +172,6 @@ python -m masster.demo.example_batch_process input_directory --recursive --dest
 
 GNU Affero General Public License v3
 
-## Contributing
-
-Contributions are welcome! Please see our contributing guidelines and code of conduct.
-
 ## Citation
 
-If you use Masster in your research, please cite:
-```
-[Citation details to be added]
-```
+If you use Masster in your research, please cite this repository.

{masster-0.2.0 → masster-0.2.2}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.2.0"
+version = "0.2.2"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.2.0 → masster-0.2.2}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.2.0"
+__version__ = "0.2.2"
 
 
 def get_version():

{masster-0.2.0 → masster-0.2.2}/src/masster/sample/h5.py

@@ -309,7 +309,7 @@ def _load_sample5(self, filename: str, map: bool = True):
             missing_columns = []
             for col in schema.get("scans_df", {}).get("columns", []):
                 if col not in scans_group:
-                    self.logger.warning(f"Column '{col}' not found in sample5/scans.")
+                    self.logger.debug(f"Column '{col}' not found in sample5/scans.")
                     data[col] = None
                     missing_columns.append(col)
                     continue
@@ -444,6 +444,14 @@ def _load_sample5(self, filename: str, map: bool = True):
                             f"Column '{col}' in scans_df not found in schema, keeping original type.",
                         )
 
+            # Ensure column order matches schema order
+            if "scans_df" in schema and "columns" in schema["scans_df"]:
+                schema_column_order = list(schema["scans_df"]["columns"].keys())
+                # Only reorder columns that exist in both schema and DataFrame
+                existing_columns = [col for col in schema_column_order if col in self.scans_df.columns]
+                if existing_columns:
+                    self.scans_df = self.scans_df.select(existing_columns)
+
             else:
                 self.scans_df = None
         else:
@@ -457,7 +465,7 @@ def _load_sample5(self, filename: str, map: bool = True):
             missing_columns = []
             for col in schema.get("features_df", {}).get("columns", []):
                 if col not in features_group:
-                    self.logger.warning(
+                    self.logger.debug(
                         f"Column '{col}' not found in sample5/features.",
                     )
                     data[col] = None
@@ -804,6 +812,14 @@ def _load_sample5(self, filename: str, map: bool = True):
                             pl.col(col).fill_nan(None).alias(col),
                         ])
 
+                # Ensure column order matches schema order
+                if "features_df" in schema and "columns" in schema["features_df"]:
+                    schema_column_order = list(schema["features_df"]["columns"].keys())
+                    # Only reorder columns that exist in both schema and DataFrame
+                    existing_columns = [col for col in schema_column_order if col in self.features_df.columns]
+                    if existing_columns:
+                        self.features_df = self.features_df.select(existing_columns)
+
             else:
                 self.features_df = None
         else:

{masster-0.2.0 → masster-0.2.2}/src/masster/sample/sample5_schema.json

@@ -1,80 +1,80 @@
 {
   "features_df": {
     "columns": {
-      "adduct": {
-        "dtype": "pl.Utf8"
-      },
-      "adduct_group": {
+      "feature_uid": {
         "dtype": "pl.Int64"
       },
-      "adduct_mass": {
-        "dtype": "pl.Float64"
+      "feature_id": {
+        "dtype": "pl.Utf8"
       },
-      "charge": {
-        "dtype": "pl.Int32"
+      "mz": {
+        "dtype": "pl.Float64"
       },
-      "chrom": {
-        "dtype": "pl.Object"
+      "rt": {
+        "dtype": "pl.Float64"
       },
-      "chrom_coherence": {
+      "rt_original": {
         "dtype": "pl.Float64"
       },
-      "chrom_height_scaled": {
+      "rt_start": {
         "dtype": "pl.Float64"
       },
-      "chrom_prominence": {
+      "rt_end": {
         "dtype": "pl.Float64"
       },
-      "chrom_prominence_scaled": {
+      "rt_delta": {
         "dtype": "pl.Float64"
       },
-      "feature_id": {
-        "dtype": "pl.Utf8"
+      "mz_start": {
+        "dtype": "pl.Float64"
       },
-      "feature_uid": {
-        "dtype": "pl.Int64"
+      "mz_end": {
+        "dtype": "pl.Float64"
       },
       "inty": {
         "dtype": "pl.Float64"
       },
+      "quality": {
+        "dtype": "pl.Float64"
+      },
+      "charge": {
+        "dtype": "pl.Int32"
+      },
       "iso": {
         "dtype": "pl.Int64"
       },
       "iso_of": {
         "dtype": "pl.Int64"
       },
-      "ms2_scans": {
-        "dtype": "pl.Object"
-      },
-      "ms2_specs": {
-        "dtype": "pl.Object"
+      "adduct_group": {
+        "dtype": "pl.Int64"
       },
-      "mz": {
-        "dtype": "pl.Float64"
+      "adduct": {
+        "dtype": "pl.Utf8"
       },
-      "mz_end": {
+      "adduct_mass": {
         "dtype": "pl.Float64"
       },
-      "mz_start": {
-        "dtype": "pl.Float64"
+      "chrom": {
+        "dtype": "pl.Object"
       },
-      "quality": {
+      "chrom_coherence": {
         "dtype": "pl.Float64"
       },
-      "rt": {
+      "chrom_prominence": {
         "dtype": "pl.Float64"
       },
-      "rt_delta": {
+      "chrom_prominence_scaled": {
         "dtype": "pl.Float64"
       },
-      "rt_end": {
+      "chrom_height_scaled": {
         "dtype": "pl.Float64"
       },
-      "rt_original": {
-        "dtype": "pl.Float64"
+      "ms2_scans": {
+        "dtype": "pl.Object"
       },
-      "rt_start": {
-        "dtype": "pl.Float64"
+      "ms2_specs": {
+        "dtype": "pl.Object"
       }
     }
   },
@@ -100,62 +100,80 @@
   },
   "scans_df": {
     "columns": {
-      "bl": {
-        "dtype": "pl.Float64"
-      },
-      "comment": {
-        "dtype": "pl.Utf8"
+      "scan_uid": {
+        "dtype": "pl.Int64"
       },
       "cycle": {
         "dtype": "pl.Int64"
       },
-      "energy": {
-        "dtype": "pl.Float64"
-      },
-      "feature_uid": {
+      "ms_level": {
         "dtype": "pl.Int64"
       },
-      "id": {
-        "dtype": "pl.Utf8"
+      "rt": {
+        "dtype": "pl.Float64"
       },
-      "inty_max": {
+      "inty_tot": {
         "dtype": "pl.Float64"
       },
       "inty_min": {
         "dtype": "pl.Float64"
       },
-      "inty_tot": {
+      "inty_max": {
         "dtype": "pl.Float64"
       },
-      "ms_level": {
-        "dtype": "pl.Int64"
-      },
-      "mz_max": {
+      "bl": {
         "dtype": "pl.Float64"
       },
       "mz_min": {
         "dtype": "pl.Float64"
       },
+      "mz_max": {
+        "dtype": "pl.Float64"
+      },
+      "comment": {
+        "dtype": "pl.Utf8"
+      },
       "name": {
         "dtype": "pl.Utf8"
       },
-      "prec_inty": {
-        "dtype": "pl.Float64"
+      "id": {
+        "dtype": "pl.Utf8"
       },
       "prec_mz": {
         "dtype": "pl.Float64"
       },
+      "prec_mz_min": {
+        "dtype": "pl.Float64"
+      },
       "prec_mz_max": {
         "dtype": "pl.Float64"
       },
-      "prec_mz_min": {
+      "prec_inty": {
         "dtype": "pl.Float64"
       },
-      "rt": {
+      "energy": {
         "dtype": "pl.Float64"
       },
-      "scan_uid": {
+      "feature_uid": {
         "dtype": "pl.Int64"
+      },
+      "ms2_n": {
+        "dtype": "pl.Int64"
+      },
+      "time_cycle": {
+        "dtype": "pl.Float64"
+      },
+      "time_ms1_to_ms1": {
+        "dtype": "pl.Float64"
+      },
+      "time_ms1_to_ms2": {
+        "dtype": "pl.Float64"
+      },
+      "time_ms2_to_ms2": {
+        "dtype": "pl.Float64"
+      },
+      "time_ms2_to_ms1": {
+        "dtype": "pl.Float64"
       }
     }
   },