masster 0.5.27__py3-none-any.whl → 0.6.1__py3-none-any.whl

{masster-0.5.27.dist-info → masster-0.6.1.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.27
+Version: 0.6.1
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
 Project-URL: documentation, https://github.com/zamboni-lab/masster#readme
 Project-URL: Third-Party Licenses, https://github.com/zamboni-lab/masster/blob/main/THIRD_PARTY_NOTICES.md
-Author: Zamboni Lab
+Author: Zamboni Lab, ETH Zurich
 License:                     GNU AFFERO GENERAL PUBLIC LICENSE
                                Version 3, 19 November 2007
         
@@ -726,17 +726,39 @@ Requires-Dist: pytest-mock>=3.10.0; extra == 'test'
 Requires-Dist: pytest>=7.0.0; extra == 'test'
 Description-Content-Type: text/markdown
 
-# MASSter
+# masster
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/masster)](https://badge.fury.io/py/masster)
 [![PyPI version](https://badge.fury.io/py/masster.svg)](https://badge.fury.io/py/masster)
 
-**MASSter** is a Python package for the analysis of mass spectrometry data, tailored for the purpose of metabolomics and LC-MS data processing. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. The sample-centric feature detection uses OpenMS. All other functionalities for e.g. centroiding, RT alignment, adduct and isotopomer detection, merging of multiple samples, gap-filling, quantification, etc. were redesigned and engineered to maximize scalability (tested with 3000 LC-MS), speed, quality, and results.
+**MASSter** is a Python package for the analysis of metabolomics experiments by LC-MS/MS data, with a main focus on the challenging tasks of untargeted and large-scale studies.  
 
-This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. 
+## Background and motivation
+
+MASSter is actively used, maintained, and developed by the Zamboni Lab at ETH Zurich. The project started because many needs were unmet by the "usual" software packages (mzMine, MS-DIAL, Workflow4Metabolomics (W4M), ...), for example performance, scalability, sensitivity, robustness, speed, rapid implementation of new features, and embedding in ETL systems.
+
+All methods include many parameters and may wrap alternative algorithms. These options are primarily relevant for advanced users. We recommend running the processing methods with the defaults or using the Wizard.
+
+## Content
+
+MASSter is designed to deal with DDA data, and hides functionalities for DIA and ZTScan DIA data. The sample-centric feature detection uses OpenMS, which is both accurate and fast, and it was wrapped with additional code to improve isotope and adduct detection. All other functionalities are own implementations: centroiding, RT alignment, adduct and isotopomer detection, merging of multiple samples, gap-filling, quantification, etc. 
+
+MASSter was engineered to maximize result quality, sensitivity, scalability, and speed. Yes, it's Python, which can be slower than other languages, but considerable effort was spent on optimizations, including the systematic use of [Polars](https://pola.rs/), NumPy vectorization, multiprocessing, and chunking. MASSter has been tested on studies with 3,000+ LC–MS/MS samples (≈1 million MS2 spectra) and autonomously completed analyses within a few hours.
+
+## Architecture
+
+MASSter defines classes for Spectra, Chromatograms, Libraries, Samples, and Studies (a Study is a collection of samples, i.e. an LC–MS sequence). Users will typically work with a single `Study` object at a time. `Sample` objects are created when analyzing a batch (and saved for caching), or used for development, troubleshooting, or generating illustrations.
+
+The analysis can be done in scripts (without user intervention, e.g. by the integrated Wizard), or interactively in notebooks, i.e. [marimo](https://marimo.io/) or [jupyter](https://jupyter.org/).
 
 ## Prerequisites
 
-**MASSter** reads raw (Thermo), wiff (SCIEX), or mzML data. It's recommended to provide raw, profile data.
+You'll need to install Python (3.10-3.13, 3.14 has not been tested yet).
+
+MASSter reads raw (Thermo), wiff (SCIEX), or mzML data. Reading vendor formats relies on .NET libraries, and is only possible in Windows. On Linux or MacOS, you'll be forced to use mzML data.
+
+**It's recommended to use data in either the vendor's raw formats (WIFF and Thermo RAW) or mzML in profile mode.** MASSter includes a sophisticated and sufficiently fast centroiding algorithm that works well across the full dynamic range and will only act on spectra that are relevant. In our tests with data from different vendors, the centroiding performed much better than most vendor implementations (which are primarily proteomics-centric).
+
+If you still want to convert raw data to centroided mzML, please use CentroidR: https://github.com/Adafede/CentroidR/tree/0.0.0.9001
 
 ## Installation
 
@@ -744,48 +766,33 @@ This is a poorly documented, stable branch of the development codebase in use in
 pip install masster
 ```
 
-## Basic usage
-### Quick start: use the wizard
+## Getting started
+**The quickest way to use, or learn how to use MASSter, is to use the Wizard** which we integrated and, ideally, takes care of everything automatically. 
 
+The Wizard only needs to know where to find the MS files and where to store the results.
 ```python
-import masster
-wiz = masster.wizard.create_scripts(
-    source=r'..\..\folder_with_raw_data',
-    folder=r'..\..folder_to_store_results'
+from masster import Wizard
+wiz = Wizard(
+    source=r'..\..\folder_with_raw_data',    # where to find the data
+    folder=r'..\..folder_to_store_results',  # where to save the results
+    ncores=10                                # this is optional
     )
-wiz.run()
+wiz.test_and_run()
 ```
 
-This will run a wizard that should perform all key steps and save the results to the `folder`.
-
-### Basic workflow for analyzing a single sample
-```python
-import masster
-sample = masster.Sample(filename='...') # full path to a *.raw, *.wiff, or *.mzML file
-# process
-sample.find_features(chrom_fwhm=0.5, noise=50) # for orbitrap data, set noise to 1e5
-sample.find_adducts()
-sample.find_ms2()
-
-# access data
-sample.features_df
+This will trigger the analysis of raw data, and the creation of a script to process all samples and then assemble the study. The whole processing will be stored as `1_masster_workflow.py` in the output folder. The wizard will test once and, if successful, run the full workflow using parallel processes. Once the processing is over you, navigate to `folder` to see what happened...
 
-# save results
-sample.save() # stores to *.sample5, our custom hdf5 format
-sample.export_mgf()
-
-# some plots
-sample.plot_bpc()
-sample.plot_tic()
-sample.plot_2d()
-sample.plot_features_stats()
+If you want to interact with your data, we recommend using [marimo](https://marimo.io/) or [jupyter](https://jupyter.org/) and open the `*.study5` file, for example:
 
-# explore methods
-dir(study)
+```bash
+# use marimo to open the script created by marimo
+marimo edit '..\\..\\folder_to_store_results\\2_interactive_analysis.py'
+# or, if you use uv to manage an environment with masster
+uv run marimo edit '..\\..\\folder_to_store_results\\2_interactive_analysis.py'
 ```
 
-### Basic Workflow for analyzing LC-MS study with 2-... samples
-
+### Basic Workflow for analyzing LC-MS study with 1-1000+ samples
+In MASSter, the main object for data analysis is a `Study`, which consists of a bunch of `Samples`. 
 ```python
 import masster
 # Initialize the Study object with the default folder
@@ -797,17 +804,20 @@ study.add(r'D:\...\...\...\*.wiff')
 # Perform retention time correction
 study.align(rt_tol=2.0)
 study.plot_alignment()
-study.plot_bpc()
 study.plot_rt_correction()
+study.plot_bpc()
 
 # Find consensus features
-study.merge(min_samples=3)
+study.merge(min_samples=3)   # this will keep only the features that were found in 3 or more samples
 study.plot_consensus_2d()
 
-# Retrieve missing data for quantification
+# retrieve information
+study.info()
+
+# Retrieve EICs for quantification
 study.fill()
 
-# Integrate according to consensus metadata
+# Integrate EICs according to consensus metadata
 study.integrate()
 
 # export results
@@ -823,32 +833,62 @@ study.save()
 study.plot_samples_pca()
 study.plot_samples_umap()
 study.plot_samples_2d()
-```
+study.plot_heatmap()
 
-### Quick Start with Wizard
-MASSter includes a Wizard to automatically process everything:
+# To know more about the available methods...
+dir(study)
+```
+The information is stored in Polars data frame, in particular:
+```python
+# information on samples
+study.samples_df
+# information on consensus features
+study.consensus_df
+# information on original features from ALL samples, including MS2 and EICs
+study.features_df
+```
 
+### Analysis of a single sample
+For troubleshooting, exploration, or just to create a figure on a single file, you might want to open and process a single file:  
 ```python
-from masster import Wizard
+from masster import Sample
+sample = Sample(filename='...') # full path to a *.raw, *.wiff, *.mzML, or *.sample5 file
+# peek into sample
+sample.info()
+
+# process
+sample.find_features(chrom_fwhm=0.5, noise=50) # for orbitrap data, set noise to 1e5
+sample.find_adducts()
+sample.find_ms2()
 
-# Create wizard instance
-wiz = Wizard(source="./raw_data", 
-             folder="./output", 
-             num_cores=8)
+# access data
+sample.features_df
 
-# Generate analysis scripts
-wiz.create_scripts()
+# save results
+sample.save() # stores to *.sample5, our custom hdf5 format
+sample.export_mgf()
 
-# Test with single file, then run full batch
-wiz.test_and_run()
-```
+# some plots
+sample.plot_bpc()
+sample.plot_tic()
+sample.plot_2d()
+sample.plot_features_stats()
 
-### One-Line Command Processing
-Or, from the command-line:
-```bash
-python -c "from masster import Wizard; wiz = Wizard(source='D:/Data/studies/my_study/raw', folder='D:/Data/studies/my_study/masster'); wiz.create_scripts(); wiz.test_and_run()"
+# explore methods
+dir(sample)
 ```
 
+## Disclaimer
+
+**MASSter is research software under active development.** While we use it extensively in our lab and strive for quality and reliability, please be aware:
+
+- **No warranties**: The software is provided "as is" without any warranty of any kind, express or implied
+- **Backward compatibility**: We do not guarantee backward compatibility between versions. Breaking changes may occur as we improve the software
+- **Performance**: While optimized for our workflows, performance may vary depending on your data and system configuration
+- **Results**: We do our best to ensure accuracy, but you should validate results independently for your research
+- **Support**: This is an academic project with limited resources. At the moment, we do not provide external user support.
+- **Production use**: If you plan to use MASSter in production or critical workflows, thorough testing with your data is recommended
+
 ## License
 GNU Affero General Public License v3
 
@@ -858,4 +898,4 @@ See the [LICENSE](LICENSE) file for details.
 This project uses several third-party libraries, including pyOpenMS which is licensed under the BSD 3-Clause License. For complete information about third-party dependencies and their licenses, see [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).
 
 ## Citation
-If you use Masster in your research, please cite this repository.
+If you use MASSter in your research, please cite this repository.

{masster-0.5.27.dist-info → masster-0.6.1.dist-info}/RECORD

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 masster/__init__.py,sha256=B7zftzdElF2Wb5B7KvkD6TONnMIY-Jxeen3s49dgmzs,1029
-masster/_version.py,sha256=1ymsIuIjSvggBFAIWxPqWntiqdxjPZEjAmDJy3vRsLE,257
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 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
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 masster/spectrum.py,sha256=LlmxrI5MFS3aPrGSdqUSKVY0rJnKeBh3Frdh6a4dPvA,49722
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 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data,sha256=01vC6m__Qqm2rLvlTMZoeKIKowFvovBTUnrNl8Uav3E,24576
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 masster/study/importers.py,sha256=iOe9w6uEn39ShosRms8n_zIrsSBczb51CAMoMrxSUw4,13587
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 masster/study/parameters.py,sha256=bTvmcwX9INxzcrEAmTiFH8qeWVhwkvMTZjuP394pz5o,3279
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 masster/study/processing.py,sha256=oQGepG5-AXP9GGk8NTzl_i1ztgDp3TPwE2x15BmnpMw,57353
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 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
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 masster/study/defaults/export_def.py,sha256=eXl3h4aoLX88XkHTpqahLd-QZ2gjUqrmjq8IJULXeWo,1203
@@ -58,11 +59,11 @@ masster/study/defaults/identify_def.py,sha256=nFj-pv6q1eRgSgoRr78YEnqulPPMWo2Ju5
 masster/study/defaults/integrate_chrom_def.py,sha256=0MNIWGTjty-Zu-NTQsIweuj3UVqEY3x1x8pK0mPwYak,7264
 masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
 masster/study/defaults/merge_def.py,sha256=99TJtIk7mSoq8NMJMJ4b-cy7gUUixQN69krxttBnkfA,12899
-masster/study/defaults/study_def.py,sha256=xXOAcb8hez0woWwA1_T3fcokjiLJkq3hwA3OS6elb6I,15965
+masster/study/defaults/study_def.py,sha256=kSvhiqpFp8b84vUsE8608LQsSXwz9lAPcU2BqK0T8z0,16095
 masster/wizard/__init__.py,sha256=L9G_datyGSFJjrBVklEVpZVLGXzUhDiWobtiygBH8vQ,669
-masster/wizard/wizard.py,sha256=11utDrZSt7R8D16Sl-NbRKHcgzhQEu8gW_q2V02-Qi0,66483
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masster/data/libs/aa.csv

@@ -1,22 +0,0 @@
-name,smiles,inchikey,formula,db_id,db
-L-Glutamic acid,N[C@@H](CCC(O)=O)C(O)=O,WHUUTDBJXJRKMK-VKHMYHEASA-N,C5H9NO4,CID:33032,pubchem
-L-Tyrosine,N[C@@H](CC1=CC=C(O)C=C1)C(O)=O,OUYCCCASQSFEME-QMMMGPOBSA-N,C9H11NO3,CID:6057,pubchem
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masster/data/libs/ccm.csv

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-"Fructose-1,6-bisphosphate",C6H13O12P,O=P(O)(O)OC[C@H]1O[C@](O)(COP(=O)(O)O)[C@@H](O)[C@@H]1O,RNBGYGVWRKECFJ-ARQDHWQXSA-N,CID:10267,pubchem
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-Methionine,C5H11NO2S,CSCC[C@H](N)C(=O)O,FFEARJCKVFRZRR-BYPYZUCNSA-N,CID:6137,pubchem
-Phenylalanine,C9H10NO,N[C@@H](Cc1ccccc1)C(=O)O,COLNVLDHVKWLRT-QMMMGPOBSA-N,CID:6140,pubchem
-Proline,C5H8NO,O=C(O)[C@@H]1CCCN1,ONIBWKKTOPOVIA-BYPYZUCNSA-N,CID:145742,pubchem
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