masster 0.2.2__tar.gz → 0.2.3__tar.gz

{masster-0.2.2 → masster-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.2.2
+Version: 0.2.3
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -736,23 +736,12 @@ Most core processing functions are derived from OpenMS. We use the same nomencla
 
 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)
-- **Feature detection and alignment**: Automated chromatographic peak detection and retention time alignment
-- **Consensus feature building**: Identification of features across multiple samples
-- **Interactive visualizations**: 2D plots, chromatograms, and statistical dashboards
-- **Batch processing**: Process entire studies with multiple samples
-- **Export capabilities**: MGF export for spectral library searches
-
 ## Installation
 
 ```bash
 pip install masster
 ```
 
-## Quick Start
-
 ### Basic Workflow for analyzing LC-MS study with 2-... samples
 
 ```python
@@ -784,114 +773,6 @@ study.export_mgf()
 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
-from masster.sample import Sample
-
-# Load a single sample (mzML, RAW, WIFF)
-sample = Sample("path/to/your/file.mzML")
-
-# Detect features
-sample.find_features(chrom_peak_snr=10, noise=500, chrom_fwhm=1.0)
-
-# Detect adducts
-sample.find_adducts()
-
-# Find MS2 spectra
-sample.find_ms2()
-
-# Save results to .sample5
-sample.save()
-```
-
-Masster provides extensive plotting capabilities for data exploration and quality control:
-
-### Single sample visualization
-
-```python
-# Plot 2D overview of MS data with detected features
-sample.plot_2d(
-    filename="overview_2d.html",
-    show_features=True,
-    show_ms2=True,
-    title="MS Data Overview"
-)
-
-# Plot with feature filtering
-sample.plot_2d(
-    filename="features_ms2_only.html"
-)
-
-# Plot extracted ion chromatogram
-sample.plot_eic(
-    feature_uid=123,
-    rt_tol=10,
-    mz_tol=0.005
-)
-```
-
-### Quality Control Plots
-
-```python
-# Plot DDA acquisition statistics
-sample.plot_dda_stats(filename="dda_stats.html")
-
-# Plot feature statistics
-sample.plot_feature_stats(filename="feature_stats.html")
-
-# Plot total ion chromatogram
-sample.plot_tic(filename="tic.html")
-```
-
-### Advanced Plotting Options
-
-```python
-# Plot with Oracle annotation data
-sample.plot_2d_oracle(
-    oracle_folder="path/to/oracle/results",
-    colorby="hg",  # Color by chemical class
-    filename="annotated_features.html"
-)
-
-# Plot MS2 cycle view
-sample.plot_ms2_cycle(
-    cycle=100,
-    filename="ms2_cycle.html",
-    centroid=True
-)
-```
-
-## File Format Support
-
-- **Input formats**: .wiff, .mzML, .raw files
-- **Intermediate formats**: .sample5 and .study5 (HDF5) for fast loading
-- **Export formats**: .mgf, .csv
-- **Visualization**: .html (interactive), .png, .svg
-
-## Advanced Features
-
-### Batch Processing
-Use the command-line interface for processing multiple files:
-
-```bash
-python -m masster.demo.example_batch_process input_directory --recursive --dest output_directory
-```
-
 ## Requirements
 
 - Python ≥ 3.11

masster-0.2.3/README.md

@@ -0,0 +1,58 @@
+# 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. 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.
+
+## Installation
+
+```bash
+pip install masster
+```
+
+### Basic Workflow for analyzing LC-MS study with 2-... samples
+
+```python
+import masster
+
+# Initialize the Study object with the default folder
+study = masster.Study(default_folder=r'D:\...\mylcms')
+
+# Load data from folder with raw data, here: WIFF
+study.add_folder(r'D:\...\...\...\*.wiff')
+
+# Align maps
+study.align(rt_max_diff=2.0)
+
+# Find consensus features
+study.find_consensus(min_samples=3)
+
+# Retrieve missing data for quantification
+study.fill_chrom(abs_)
+
+# Integrate according to consensus metadata
+study.integrate_chrom()
+
+# link MS2 across the whole study and export them
+study.find_ms2()
+study.export_mgf()
+
+# Save the study to .study5
+study.save()
+```
+
+## Requirements
+
+- Python ≥ 3.11
+- Key dependencies: pandas, polars, numpy, scipy, matplotlib, bokeh, holoviews, panel
+- See `pyproject.toml` for complete dependency list
+
+## License
+
+GNU Affero General Public License v3
+
+## Citation
+
+If you use Masster in your research, please cite this repository.

{masster-0.2.2 → masster-0.2.3}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.2.2"
+version = "0.2.3"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.2.2 → masster-0.2.3}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.2.2"
+__version__ = "0.2.3"
 
 
 def get_version():

{masster-0.2.2 → masster-0.2.3}/src/masster/study/save.py

@@ -122,12 +122,6 @@ def _save_consensusXML(self, filename:str):
         return
 
     fh = oms.ConsensusXMLFile()
-    # check if filename includes any path
-    if not os.path.isabs(filename):
-        if self.default_folder is not None:
-            filename = os.path.join(self.default_folder, filename)
-        else:
-            filename = os.path.join(os.getcwd(), filename)
     fh.store(filename, self.consensus_map)
     self.logger.info(f"Saved consensus map to {filename}")
 

{masster-0.2.2 → masster-0.2.3}/src/masster/study/study.py

@@ -147,6 +147,7 @@ class Study:
 
     def __init__(
         self,
+        filename=None,
         **kwargs,
     ):
         """
@@ -156,6 +157,10 @@ class Study:
         data storage, and processing parameters used for study-level analysis.
 
         Parameters:
+            filename (str, optional): Path to a .study5 file to load automatically.
+                                    If provided, the default_folder will be set to the
+                                    directory containing this file, and the study will
+                                    be loaded automatically.
             **kwargs: Keyword arguments for setting study parameters. Can include:
                      - A study_defaults instance to set all parameters at once (pass as params=study_defaults(...))
                      - Individual parameter names and values (see study_defaults for available parameters)
@@ -172,6 +177,20 @@ class Study:
         """
         # Initialize default parameters
 
+        # Handle filename parameter for automatic loading
+        auto_load_filename = None
+        if filename is not None:
+            if not filename.endswith('.study5'):
+                raise ValueError("filename must be a .study5 file")
+            if not os.path.exists(filename):
+                raise FileNotFoundError(f"Study file not found: {filename}")
+            
+            # Set default_folder to the directory containing the file if not already specified
+            if 'default_folder' not in kwargs:
+                kwargs['default_folder'] = os.path.dirname(os.path.abspath(filename))
+            
+            auto_load_filename = filename
+
         # Check if a study_defaults instance was passed
         if "params" in kwargs and isinstance(kwargs["params"], study_defaults):
             params = kwargs.pop("params")
@@ -234,6 +253,10 @@ class Study:
             sink=self.log_sink
         )
 
+        # Auto-load study file if filename was provided
+        if auto_load_filename is not None:
+            self.load(filename=auto_load_filename)
+
     
 
     # Attach module functions as class methods  

{masster-0.2.2 → masster-0.2.3}/uv.lock

@@ -1585,7 +1585,7 @@ wheels = [
 
 [[package]]
 name = "masster"
-version = "0.2.2"
+version = "0.2.3"
 source = { editable = "." }
 dependencies = [
     { name = "alphabase" },

masster-0.2.2/README.md

@@ -1,177 +0,0 @@
-# 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. 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)
-- **Feature detection and alignment**: Automated chromatographic peak detection and retention time alignment
-- **Consensus feature building**: Identification of features across multiple samples
-- **Interactive visualizations**: 2D plots, chromatograms, and statistical dashboards
-- **Batch processing**: Process entire studies with multiple samples
-- **Export capabilities**: MGF export for spectral library searches
-
-## Installation
-
-```bash
-pip install masster
-```
-
-## Quick Start
-
-### Basic Workflow for analyzing LC-MS study with 2-... samples
-
-```python
-import masster
-
-# Initialize the Study object with the default folder
-study = masster.Study(default_folder=r'D:\...\mylcms')
-
-# Load data from folder with raw data, here: WIFF
-study.add_folder(r'D:\...\...\...\*.wiff')
-
-# Align maps
-study.align(rt_max_diff=2.0)
-
-# Find consensus features
-study.find_consensus(min_samples=3)
-
-# Retrieve missing data for quantification
-study.fill_chrom(abs_)
-
-# Integrate according to consensus metadata
-study.integrate_chrom()
-
-# link MS2 across the whole study and export them
-study.find_ms2()
-study.export_mgf()
-
-# 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
-from masster.sample import Sample
-
-# Load a single sample (mzML, RAW, WIFF)
-sample = Sample("path/to/your/file.mzML")
-
-# Detect features
-sample.find_features(chrom_peak_snr=10, noise=500, chrom_fwhm=1.0)
-
-# Detect adducts
-sample.find_adducts()
-
-# Find MS2 spectra
-sample.find_ms2()
-
-# Save results to .sample5
-sample.save()
-```
-
-Masster provides extensive plotting capabilities for data exploration and quality control:
-
-### Single sample visualization
-
-```python
-# Plot 2D overview of MS data with detected features
-sample.plot_2d(
-    filename="overview_2d.html",
-    show_features=True,
-    show_ms2=True,
-    title="MS Data Overview"
-)
-
-# Plot with feature filtering
-sample.plot_2d(
-    filename="features_ms2_only.html"
-)
-
-# Plot extracted ion chromatogram
-sample.plot_eic(
-    feature_uid=123,
-    rt_tol=10,
-    mz_tol=0.005
-)
-```
-
-### Quality Control Plots
-
-```python
-# Plot DDA acquisition statistics
-sample.plot_dda_stats(filename="dda_stats.html")
-
-# Plot feature statistics
-sample.plot_feature_stats(filename="feature_stats.html")
-
-# Plot total ion chromatogram
-sample.plot_tic(filename="tic.html")
-```
-
-### Advanced Plotting Options
-
-```python
-# Plot with Oracle annotation data
-sample.plot_2d_oracle(
-    oracle_folder="path/to/oracle/results",
-    colorby="hg",  # Color by chemical class
-    filename="annotated_features.html"
-)
-
-# Plot MS2 cycle view
-sample.plot_ms2_cycle(
-    cycle=100,
-    filename="ms2_cycle.html",
-    centroid=True
-)
-```
-
-## File Format Support
-
-- **Input formats**: .wiff, .mzML, .raw files
-- **Intermediate formats**: .sample5 and .study5 (HDF5) for fast loading
-- **Export formats**: .mgf, .csv
-- **Visualization**: .html (interactive), .png, .svg
-
-## Advanced Features
-
-### Batch Processing
-Use the command-line interface for processing multiple files:
-
-```bash
-python -m masster.demo.example_batch_process input_directory --recursive --dest output_directory
-```
-
-## Requirements
-
-- Python ≥ 3.11
-- Key dependencies: pandas, polars, numpy, scipy, matplotlib, bokeh, holoviews, panel
-- See `pyproject.toml` for complete dependency list
-
-## License
-
-GNU Affero General Public License v3
-
-## Citation
-
-If you use Masster in your research, please cite this repository.