masster 0.5.17__py3-none-any.whl → 0.5.19__py3-none-any.whl

masster/study/study.py

@@ -905,6 +905,7 @@ class Study:
             f"Study folder:           {self.folder}\n"
             f"Last save:              {self.filename}\n"
             f"Samples:                {samples_df_len}\n"
+            f"Polarity:               {self.polarity}\n"
             f"Features:               {unfilled_features_count}\n"
             f"- in consensus:         {ratio_in_consensus_to_total:.0f}%\n"
             f"- not in consensus:     {ratio_not_in_consensus_to_total:.0f}%\n"

masster/wizard/README.md

@@ -12,7 +12,7 @@ from masster import Wizard
 # Create wizard with minimal configuration
 wizard = Wizard(
     data_source="./raw_data",      # Directory with raw files
-    study_folder="./processed",    # Output directory  
+    study_folder="./processed",    # Output directory
     polarity="positive",           # or "negative"
     num_cores=4                    # CPU cores to use
 )
@@ -35,22 +35,22 @@ params = wizard_def(
     study_folder="./processed_advanced",
     polarity="negative",
     num_cores=8,
-    
+
     # File discovery
     file_extensions=[".wiff", ".raw", ".mzML"],
     search_subfolders=True,
     skip_patterns=["blank", "QC", "test"],
-    
+
     # Processing parameters
     adducts=["H-1:-:0.95", "Cl:-:0.05", "CH2O2:0:0.2"],
     chrom_fwhm=0.15,
     noise_threshold=5e4,
-    
+
     # Study assembly
     rt_tolerance=1.0,
     mz_tolerance=0.008,
     min_samples_for_merge=30,
-    
+
     # Output options
     export_formats=["csv", "xlsx", "mgf", "parquet"],
     generate_plots=True,
@@ -73,7 +73,7 @@ wizard.run_full_pipeline()
 
 ### 💾 Intelligent Resume
 - **Checkpoint System**: Automatically saves progress at key points
-- **File Tracking**: Remembers which files have been processed successfully  
+- **File Tracking**: Remembers which files have been processed successfully
 - **Smart Recovery**: Resumes from last successful step after interruption
 - **Validation**: Verifies existing outputs before skipping
 
@@ -112,7 +112,7 @@ wizard.run_full_pipeline()
 
 ### 4. Feature Alignment
 - **RT Alignment**: Corrects retention time shifts between samples
-- **Mass Alignment**: Accounts for mass calibration differences  
+- **Mass Alignment**: Accounts for mass calibration differences
 - **Algorithm Selection**: Supports KD-tree, QT-clustering, and chunked methods
 - **Validation**: Reports alignment statistics and quality metrics
 
@@ -232,7 +232,7 @@ Returns detailed status dictionary with current step, processed files, timing, a
 - Ensure sufficient disk space in output directory
 - Close any applications that might lock files
 
-**Processing Failures** 
+**Processing Failures**
 - Check individual file integrity
 - Review `skip_patterns` to exclude problematic files
 - Examine detailed logs in `wizard.log` and `processing.log`
@@ -249,7 +249,7 @@ The Wizard includes built-in validation at each step:
 
 - **File Validation**: Checks file accessibility and format compatibility
 - **Processing Validation**: Verifies sample5 outputs can be loaded
-- **Study Validation**: Ensures study assembly completed successfully  
+- **Study Validation**: Ensures study assembly completed successfully
 - **Alignment Validation**: Reports alignment statistics and warnings
 - **Export Validation**: Confirms all requested outputs were created
 
@@ -257,7 +257,7 @@ The Wizard includes built-in validation at each step:
 
 ### System Requirements
 - **Minimum**: 4 CPU cores, 8 GB RAM
-- **Recommended**: 8+ CPU cores, 16+ GB RAM  
+- **Recommended**: 8+ CPU cores, 16+ GB RAM
 - **Large Studies**: 16+ CPU cores, 32+ GB RAM
 - **Storage**: SSD recommended, ~2-3x raw data size free space
 
@@ -265,7 +265,7 @@ The Wizard includes built-in validation at each step:
 
 **For Small Studies (< 50 samples)**
 - Use `num_cores = 4-6`
-- Set `batch_size = 4-8`  
+- Set `batch_size = 4-8`
 - Use `merge_method = "kd"`
 - Enable all export formats
 
@@ -297,7 +297,7 @@ if not wizard.study_folder_path.glob("*.sample5"):
 
 # Continue with study-level processing
 wizard.assemble_study()
-wizard.align_and_merge() 
+wizard.align_and_merge()
 wizard.export_results()
 ```
 
@@ -312,7 +312,7 @@ studies = [
 for study_config in studies:
     wizard = Wizard(**study_config, num_cores=8)
     success = wizard.run_full_pipeline()
-    
+
     if success:
         print(f"✅ {study_config['output']} completed")
     else:
@@ -338,7 +338,7 @@ if hasattr(wizard.study, 'features_filter'):
     )
     wizard.study.features_filter(selection)
 
-# Continue with standard pipeline  
+# Continue with standard pipeline
 wizard.align_and_merge()
 wizard.generate_plots()
 ```
@@ -370,4 +370,4 @@ The Wizard generates several types of output files:
 - `sample_name.mgf` - Individual sample MS2 spectra
 - `sample_name_2d.html` - Individual sample 2D plot
 
-The Wizard provides a complete, automated solution for mass spectrometry data processing while maintaining flexibility for custom workflows and providing robust error handling and recovery capabilities.
+The Wizard provides a complete, automated solution for mass spectrometry data processing while maintaining flexibility for custom workflows and providing robust error handling and recovery capabilities.

masster/wizard/wizard.py

@@ -66,7 +66,7 @@ class wizard_def:
         # Core Configuration
         source (str): Path to directory containing raw data files
         folder (str): Output directory for processed study
-        polarity (str): Ion polarity mode ("positive" or "negative")
+        polarity (Optional[str]): Ion polarity mode ("positive", "negative", or None for auto-detection)
         num_cores (int): Number of CPU cores to use for parallel processing
         
         # File Discovery
@@ -98,7 +98,7 @@ class wizard_def:
     # === Core Configuration ===
     source: str = ""
     folder: str = ""  
-    polarity: str = "positive"
+    polarity: Optional[str] = None
     num_cores: int = 4
     
     # === File Discovery ===
@@ -198,12 +198,12 @@ class wizard_def:
         """Set polarity-specific defaults after initialization."""
         # Set default adducts based on polarity if not provided
         if not self.adducts:
-            if self.polarity.lower() in ["positive", "pos"]:
+            if self.polarity and self.polarity.lower() in ["positive", "pos"]:
                 self.adducts = ["H:+:0.8", "Na:+:0.1", "NH4:+:0.1"]
-            elif self.polarity.lower() in ["negative", "neg"]: 
+            elif self.polarity and self.polarity.lower() in ["negative", "neg"]: 
                 self.adducts = ["H-1:-:1.0", "CH2O2:0:0.5"]
             else:
-                # Default to positive
+                # Default to positive if polarity is None or unknown
                 self.adducts = ["H:+:0.8", "Na:+:0.1", "NH4:+:0.1"]
         
         # Validate num_cores
@@ -245,7 +245,7 @@ class Wizard:
         self,
         source: str = "",
         folder: str = "",
-        polarity: str = "positive",
+        polarity: Optional[str] = None,
         adducts: Optional[List[str]] = None,
         num_cores: int = 6,
         **kwargs
@@ -256,7 +256,7 @@ class Wizard:
         Parameters:
             source: Directory containing raw data files
             folder: Output directory for processed study
-            polarity: Ion polarity mode ("positive" or "negative")
+            polarity: Ion polarity mode ("positive", "negative", or None for auto-detection)
             adducts: List of adduct specifications (auto-set if None)
             num_cores: Number of CPU cores (0 = auto-detect 75% of available)
             **kwargs: Additional parameters (see wizard_def for full list)
@@ -298,8 +298,8 @@ class Wizard:
         self.folder_path = Path(self.params.folder) 
         self.folder_path.mkdir(parents=True, exist_ok=True)
         
-        # Auto-infer polarity from the first file if not explicitly set by user
-        if polarity == "positive" and "polarity" not in kwargs:
+        # Auto-infer polarity from the first file if polarity is None
+        if self.params.polarity is None:
             inferred_polarity = self._infer_polarity_from_first_file()
             if inferred_polarity:
                 self.params.polarity = inferred_polarity
@@ -311,7 +311,7 @@ class Wizard:
         Infer polarity from the first available raw data file.
         
         Returns:
-            Inferred polarity string ("positive" or "negative") or None if detection fails
+            Inferred polarity string ("positive" or "negative") or "positive" as fallback
         """
         try:
             # Find first file
@@ -324,31 +324,85 @@ class Wizard:
             else:
                 return 'positive'
 
-            # Only implement for .wiff files initially (most common format)
+            # Handle different file formats
             if first_file.suffix.lower() == '.wiff':
-                from masster.sample.load import _wiff_to_dict
-                
-                # Extract metadata from first file
-                metadata_df = _wiff_to_dict(str(first_file))
-                
-                if not metadata_df.empty and 'polarity' in metadata_df.columns:
-                    # Get polarity from first experiment  
-                    first_polarity = metadata_df['polarity'].iloc[0]
-                    
-                    # Convert numeric polarity codes to string
-                    if first_polarity == 1 or str(first_polarity).lower() in ['positive', 'pos', '+']:
-                        return "positive"
-                    elif first_polarity == -1 or str(first_polarity).lower() in ['negative', 'neg', '-']:
-                        return "negative"
+                return self._infer_polarity_from_wiff(str(first_file))
+            elif first_file.suffix.lower() == '.raw':
+                return self._infer_polarity_from_raw(str(first_file))
+            elif first_file.suffix.lower() == '.mzml':
+                return self._infer_polarity_from_mzml(str(first_file))
                     
         except Exception:
             # Silently fall back to default if inference fails
             pass
             
         return 'positive'
+        
+    def _infer_polarity_from_wiff(self, filename: str) -> str:
+        """Infer polarity from WIFF file."""
+        try:
+            from masster.sample.load import _wiff_to_dict
+            
+            # Extract metadata from first file
+            metadata_df = _wiff_to_dict(filename)
+            
+            if not metadata_df.empty and 'polarity' in metadata_df.columns:
+                # Get polarity from first experiment  
+                first_polarity = metadata_df['polarity'].iloc[0]
+                
+                # Convert numeric polarity codes to string
+                if first_polarity == 1 or str(first_polarity).lower() in ['positive', 'pos', '+']:
+                    return "positive"
+                elif first_polarity == -1 or str(first_polarity).lower() in ['negative', 'neg', '-']:
+                    return "negative"
+        except Exception:
+            pass
+        return 'positive'
+        
+    def _infer_polarity_from_raw(self, filename: str) -> str:
+        """Infer polarity from Thermo RAW file."""
+        try:
+            from masster.sample.thermo import ThermoRawFileReader
+            
+            with ThermoRawFileReader(filename) as raw_reader:
+                # Get polarity from first scan
+                first_scan = 1
+                polarity = raw_reader.get_polarity_from_scan_event(first_scan)
+                if polarity in ['positive', 'negative']:
+                    return polarity
+        except Exception:
+            pass
+        return 'positive'
+        
+    def _infer_polarity_from_mzml(self, filename: str) -> str:
+        """Infer polarity from mzML file."""
+        try:
+            # Import pyopenms with warnings suppression
+            import warnings
+            with warnings.catch_warnings():
+                warnings.filterwarnings("ignore", message=".*OPENMS_DATA_PATH.*", category=UserWarning)
+                import pyopenms as oms
+            
+            # Load the first few spectra to check polarity
+            omsexp = oms.MSExperiment()
+            oms.MzMLFile().load(filename, omsexp)
+            
+            if omsexp.getNrSpectra() > 0:
+                first_spectrum = omsexp.getSpectra()[0]
+                try:
+                    pol = first_spectrum.getInstrumentSettings().getPolarity()
+                    if pol == 1:
+                        return "positive"
+                    elif pol == 2:
+                        return "negative"
+                except Exception:
+                    pass
+        except Exception:
+            pass
+        return 'positive'
 
     @property
-    def polarity(self) -> str:
+    def polarity(self) -> Optional[str]:
         """Get the ion polarity mode."""
         return self.params.polarity
 
@@ -1323,7 +1377,7 @@ class Wizard:
 def create_scripts(
     source: str = "", 
     folder: str = "", 
-    polarity: str = "positive",
+    polarity: Optional[str] = None,
     adducts: Optional[List[str]] = None,
     num_cores: int = 0,
     **kwargs
@@ -1337,7 +1391,7 @@ def create_scripts(
     Parameters:
         source: Directory containing raw data files
         folder: Output directory for processed study
-        polarity: Ion polarity mode ("positive" or "negative")
+        polarity: Ion polarity mode ("positive", "negative", or None for auto-detection)
         adducts: List of adduct specifications (auto-set if None)
         num_cores: Number of CPU cores (0 = auto-detect)
         **kwargs: Additional parameters

{masster-0.5.17.dist-info → masster-0.5.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.17
+Version: 0.5.19
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -747,10 +747,11 @@ pip install masster
 
 ```python
 import masster
-masster.wizard.execute(
+wiz = masster.wizard.create_scripts(
     source=r'..\..\folder_with_raw_data',
     folder=r'..\..folder_to_store_results'
     )
+wiz.run()
 ```
 
 This will run a wizard that should perform all key steps and save the results to the `folder`.

{masster-0.5.17.dist-info → masster-0.5.19.dist-info}/RECORD

@@ -1,5 +1,5 @@
 masster/__init__.py,sha256=B7zftzdElF2Wb5B7KvkD6TONnMIY-Jxeen3s49dgmzs,1029
-masster/_version.py,sha256=KD2SEuC2rjv2RLni1gIwB7iF2uzGndbyPLJm7M_E38U,257
+masster/_version.py,sha256=uCkE1NJ7J1aQrPg6o1mVRwVi9N10aB8nbGRTr0cwkNY,257
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=XT2gUcUIct8LWzTp9n484g5MaB89toT76CGA41oBvfA,18375
 masster/spectrum.py,sha256=TWIgDcl0lveG40cLVZTWGp8-FxMolu-P8EjZyRBtXL4,49850
@@ -19,39 +19,40 @@ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecR
 masster/lib/__init__.py,sha256=TcePNx3SYZHz6763TL9Sg4gUNXaRWjlrOtyS6vsu-hg,178
 masster/lib/lib.py,sha256=cDV4bL2Ax0WWZReiTYze0W6XVMTJRC9DMlVYd6piRIs,38934
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/adducts.py,sha256=HDqb8QMpImRr3lZePE4GO1glA1C9ApyDVTDbr839XMk,32965
-masster/sample/h5.py,sha256=X5VBHBpgJ2FJc9mtCggJ1HSQ3ujRmb1Wnpr9sJ8bGVA,115445
+masster/sample/adducts.py,sha256=SU6S3pyyLQUSg6yPcdj3p4MfwNDsp0_FYwYYb7F4li0,33798
+masster/sample/h5.py,sha256=0FE6eH9n8RaO59HjKnFo0kKmr8L44UOQIBqcpD3LW0s,117749
 masster/sample/helpers.py,sha256=Mt9LX-Dy1Xro1a_Sy6nxQzCkP_-q7nK4xVnNm44v7UA,43872
-masster/sample/lib.py,sha256=E-j9c3Wd8f9a-H8xj7CAOwlA8KcyXPoFyYm3c8r7LtI,33755
-masster/sample/load.py,sha256=swjRBCoFGni9iPztHIKPVB5ru_xDMVryB_inPXdujTw,51819
+masster/sample/lib.py,sha256=jrzqvglaCGzZQSSRXEQXYSJ_UTaFMdpSQbWiZd1DJyc,33976
+masster/sample/load.py,sha256=GP8oYICEqHdog9_sFPiBJVwdy7foavVF7g1ffZ729-s,48711
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
 masster/sample/plot.py,sha256=5qn2Cpl363f3hW1ZeI4BZV9_36VLx39PKQMrebJhfp4,104864
-masster/sample/processing.py,sha256=mKm73pscK7L1o0DS3X957LeOBoYiCe9b2-P8mCPX8gk,56333
+masster/sample/processing.py,sha256=iPbkC2yxBZZfDkXb4xl12qeu0Z1qwm0VLQfk3bQq33w,56322
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=pw4fIE5gecdupZOOWFUiRCs0x-3qa3Nv7V_UdJ-CAsc,22202
+masster/sample/sample.py,sha256=Khhjcd1okZBxVM6bOvGV4ZU-FUagiqgZjkWm3afhECs,22365
 masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
 masster/sample/save.py,sha256=pbiRoWEA2DnhDKmMJncjveNlBqizJLOVRm5cug4ZwyM,38658
-masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
+masster/sample/sciex.py,sha256=1jwy40Ime4wPWiyfGHVnlaY8Q8dkHdQ9aGafvumdYoI,21771
+masster/sample/thermo.py,sha256=X5yDVWroHOFkWvugezrcCV5ZKPVcpTX5VKEvFSJK1vU,28128
 masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
 masster/sample/defaults/find_adducts_def.py,sha256=Bu2KiBJRxD0SAnOPNMm_Nk-6fx6QYoRXjFNGzz-0_o0,13570
 masster/sample/defaults/find_features_def.py,sha256=Bcd39uav1BniwKgrsB-I1maF3ljf4Wb1f5yv0pDYfts,17745
-masster/sample/defaults/find_ms2_def.py,sha256=KTELMAnioGLYbhzAwOgK14TZqboPEvzeBN0HC-v0Z5A,9872
+masster/sample/defaults/find_ms2_def.py,sha256=mr_XtzlhYfXt7kYWVFPt1ReGqHZQDPXe-1pGND2VvV8,9844
 masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
-masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb5iMQL0iY,14579
+masster/sample/defaults/sample_def.py,sha256=XJPtQPqgkpaLEng3eqBPznCwcKVPJSw3FC6wNVcEu5E,15460
 masster/study/__init__.py,sha256=55axdFuqRX4aXtJ8ocnhcLB32fNtmmJpCi58moO0r4g,237
 masster/study/analysis.py,sha256=L-wXBnGZCLB5UUDrjIdOiMG9zdej3Tw_SftcEmmTukM,84264
 masster/study/export.py,sha256=c1HJdLAM6Ply0n8f0DjMk4mXd9lOYePr60UJTBksUho,60092
 masster/study/h5.py,sha256=bznE9kKEfLNo0QtbyC6a6snfnR3Zjkx5BcjBNbRVlJ8,99579
 masster/study/helpers.py,sha256=FdvQV-CgQyBhXMqk6_92aKSBsZhJBK4joLxEdKzmuhw,192011
-masster/study/id.py,sha256=_ZqPz3dWZ-o7mIE0eW1cWQV8xdcdgJUaf1TT7paG5SU,90716
+masster/study/id.py,sha256=GtOyu5vuK8utydpZn-zNjTbHZsEabqAUGrCwVbauzWA,90844
 masster/study/importers.py,sha256=1Oco0yMid_siMMZdK7rQlhS20XikgjBBNAirbTHx5O8,13958
-masster/study/load.py,sha256=BMjoUDkXNI6iU2tRE2eBRzxMrvW0gRyLepqYOWaMPXU,101192
+masster/study/load.py,sha256=EsKpxUuduu-w1TREfHTYxRdEncWTd15h2IwoB3D_nuc,72070
 masster/study/merge.py,sha256=SwrsbcoI6hIuepvTJEFNoXncwMx1XXr6FVOvkSyfIbs,169239
 masster/study/parameters.py,sha256=bTvmcwX9INxzcrEAmTiFH8qeWVhwkvMTZjuP394pz5o,3279
 masster/study/plot.py,sha256=RXuTlL-jpdLn9aRrxNvTrRU8Zr4504pia-BEWYzpSfY,114048
 masster/study/processing.py,sha256=5b8K4tP-Xu1-mhdf0om-m-g65Z9Uz3Dp4UBhuMLh0yU,58627
 masster/study/save.py,sha256=47AP518epJJ9TjaGGyrLKsMsyjIk8_J4ka7bmsnRtFQ,9268
-masster/study/study.py,sha256=pu6JQKvrT2AVKhAixlt3vfaKzJqbJfBY3xPt6-MWdyU,38833
+masster/study/study.py,sha256=Qt1ltc20LRjPvfuwHLX3AGszNAzZG3t7oM0GbS6Ixbc,38891
 masster/study/study5_schema.json,sha256=uLA9TIb5loki87_BEdwSNyPYahwOanacYisXdIK0_Z0,8044
 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
 masster/study/defaults/align_def.py,sha256=Du0F592ej2einT8kOx8EUs610axSvur8_-6N19O-uJY,10209
@@ -64,12 +65,12 @@ masster/study/defaults/integrate_chrom_def.py,sha256=0MNIWGTjty-Zu-NTQsIweuj3UVq
 masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
 masster/study/defaults/merge_def.py,sha256=krR099IkENLlJVxpSjdje3E6h-_qtlc3Ep6Hpy6inrU,12978
 masster/study/defaults/study_def.py,sha256=h8dYbi9xv0sesCSQik49Z53IkskMmNtW6ixl7it5pL0,16033
-masster/wizard/README.md,sha256=mL1A3YWJZOefpJ6D0-HqGLkVRmUlOpwyVFdvJBeeoZM,14149
+masster/wizard/README.md,sha256=RX3uxT1qD5i9iDSznZUbnukixonqr96JlUE4TwssAgY,14111
 masster/wizard/__init__.py,sha256=L9G_datyGSFJjrBVklEVpZVLGXzUhDiWobtiygBH8vQ,669
 masster/wizard/example.py,sha256=xEZFTH9UZ8HKOm6s3JL8Js0Uw5ChnISWBHSZCL32vsM,7983
-masster/wizard/wizard.py,sha256=_co4abB8lNNryfqwS3AZtw6TGxw6NLowRjLXTUzJA0o,62994
-masster-0.5.17.dist-info/METADATA,sha256=SnOZZo7h6E7XV_AIjomMkMYAwbibu23vZYyhQnRMEOM,45130
-masster-0.5.17.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.5.17.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.5.17.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.5.17.dist-info/RECORD,,
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