masster 0.2.2__py3-none-any.whl → 0.2.3__py3-none-any.whl

masster/_version.py

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

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/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.dist-info → masster-0.2.3.dist-info}/METADATA

@@ -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-0.2.2.dist-info → masster-0.2.3.dist-info}/RECORD

@@ -1,5 +1,5 @@
 masster/__init__.py,sha256=xeh-hwR_2umE0CpRXn8t22wbkt4IT-FBEzeJknL8J6c,670
-masster/_version.py,sha256=CE1l1ajIZe8NnlO_z6wnQkbMvTvA7ky9zk-mlENBeo4,239
+masster/_version.py,sha256=-QmvlpTZa_4FtjijQydS9z8bCyNLc0Gv3QiTHg5Ncro,239
 masster/chromatogram.py,sha256=f25rMrNvCQN0A93wp9QPdG3H4FiOlYPbRY3H4yd7Q5Y,18910
 masster/logger.py,sha256=9uzuVEPwQkVlnsqT_eVvh33FZY_FIm3Wn2TaJcGhZP8,10674
 masster/spectrum.py,sha256=XiClDcN1uiG-_2TIr7Bqp7x8gWvHPbC5oh3zUu3fr6Y,46789
@@ -32,8 +32,8 @@ masster/study/load.py,sha256=rTmm5E-UsTg0SJqwa4i4II5ca82m8OEn05yWW2G_YPc,38718
 masster/study/parameters.py,sha256=iKCIf7_bivi0Jkz4hreKmCyusXpQX5IIuuhnmS52-Q4,3177
 masster/study/plot.py,sha256=nY6zWKUOhlyDHra4BI0c8dx7PX5fHFW8v2Ma9YpscvU,21437
 masster/study/processing.py,sha256=PjfpsVASaR0uSE4vqKzBppq4jM3HexzbGw_bn5kDwdA,42552
-masster/study/save.py,sha256=hfbYoGMaBwKPvoTm5eV3OJoSw7o3Rbed68S4RaEz1I8,5053
-masster/study/study.py,sha256=jScjivP6UyBvF_BoNpPeJq2Q_ON0wtPxCVldqAEwCOU,20376
+masster/study/save.py,sha256=_DmnAwhlZQRNeVDLNER63pXVhinV-poKMvJlIz6Bt-Y,4791
+masster/study/study.py,sha256=gXc1j4wljbw-Zx-JPsyYO86EoXPaR0N7D2GepJZOPhA,21530
 masster/study/study5_schema.json,sha256=7LfsgI-dZGpoaPiAy0kh6gDJL4yKuA7-7PHbo9j4A6E,4630
 masster/study/defaults/__init__.py,sha256=wkul1Qq83nPHI5XebWvu3yKjp5tF8OdZDJJho8r2_qA,569
 masster/study/defaults/align_def.py,sha256=8Itwit6gaqVhF9A3w9V-uqgKlcQE6uCXyC3ul_gPWFo,8872
@@ -43,8 +43,8 @@ masster/study/defaults/find_consensus_def.py,sha256=artvErq4w07SfHB0WHi68ZjxGg0X
 masster/study/defaults/find_ms2_def.py,sha256=k-GmnCKgQuVO6M-EAjzGOqgdFrqZviRaNAdiFmwVujY,4907
 masster/study/defaults/integrate_chrom_def.py,sha256=FY9QdJpdWe18sYucrwNKoZYY0eoOo0a_hcdkZHm_W00,7107
 masster/study/defaults/study_def.py,sha256=SzUzd2YTGDGCHNMR-Dw57j5PprEnPhpITonv7wx6HQA,9035
-masster-0.2.2.dist-info/METADATA,sha256=YDUoFk7NrZYKgoPNkStSPn7G9jCbtKrLxxa9Q-fBKF8,47089
-masster-0.2.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.2.2.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.2.2.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
-masster-0.2.2.dist-info/RECORD,,
+masster-0.2.3.dist-info/METADATA,sha256=hYc0JozT_r5KPMj4znX9ee0omRbd1p8sK9SU9OaIEm8,44324
+masster-0.2.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.2.3.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.2.3.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
+masster-0.2.3.dist-info/RECORD,,