masster 0.4.21__py3-none-any.whl → 0.5.0__py3-none-any.whl

{masster-0.4.21.dist-info → masster-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.21
+Version: 0.5.0
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -686,6 +686,7 @@ Requires-Dist: bokeh>=3.7.3
 Requires-Dist: cmap>=0.6.2
 Requires-Dist: datashader>=0.18.1
 Requires-Dist: h5py>=3.14.0
+Requires-Dist: hdbscan>=0.8.40
 Requires-Dist: holoviews>=1.21.0
 Requires-Dist: hvplot>=0.11.3
 Requires-Dist: loguru>=0.7.3
@@ -701,6 +702,7 @@ Requires-Dist: pythonnet>=3.0.0
 Requires-Dist: scikit-learn>=1.7.1
 Requires-Dist: scipy>=1.12.0
 Requires-Dist: tqdm>=4.65.0
+Requires-Dist: umap-learn>=0.5.9.post2
 Provides-Extra: dev
 Requires-Dist: bandit>=1.7.0; extra == 'dev'
 Requires-Dist: black>=23.0.0; extra == 'dev'
@@ -726,12 +728,13 @@ 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. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. 
+**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.
 
 This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. 
 
-Some of the 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.
+## Prerequisites
 
+**MASSter** reads raw (Thermo), wiff (SCIEX), or mzML data. It's recommended to provide raw, profile data.
 
 ## Installation
 
@@ -739,20 +742,60 @@ Some of the core processing functions are derived from OpenMS. We use the same n
 pip install masster
 ```
 
-### Basic Workflow for analyzing LC-MS study with 2-... samples
+## Basic usage
+### Quick start: use the wizard
+
+```python
+import masster
+masster.wizard.execute(
+    source=r'..\..\folder_with_raw_data',
+    folder=r'..\..folder_to_store_results'
+    )
+```
 
+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
+
+# 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()
+
+# explore methods
+dir(study)
+```
+
+### 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')
+study = masster.Study(folder=r'D:\...\mylcms')
 
 # Load data from folder with raw data, here: WIFF
 study.add(r'D:\...\...\...\*.wiff')
 
 # Perform retention time correction
-study.align(rt_max_diff=2.0)
+study.align(rt_tol=2.0)
 study.plot_alignment()
+study.plot_bpc()
+study.plot_rt_correction()
 
 # Find consensus features
 study.merge(min_samples=3)
@@ -772,18 +815,15 @@ study.export_parquet()
 
 # 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
+# Some of the plots...
+study.plot_samples_pca()
+study.plot_samples_umap()
+study.plot_samples_2d()
+```
 
 ## License
-
 GNU Affero General Public License v3
 
 ## Citation
-
 If you use Masster in your research, please cite this repository.

{masster-0.4.21.dist-info → masster-0.5.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
 masster/__init__.py,sha256=ueZ224WPNRRjQEYTaQUol818nwQgJwB93HbEfmtPRmg,1041
-masster/_version.py,sha256=y5IX-RaakVoxIcxnpOMo4HnIGk-qPigff8Q07QC6yJU,257
+masster/_version.py,sha256=P5MV1QkrG88uczENqaXQiyOnJWkFQaZ4FsWNCqYySbg,256
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=tR65N23zfrNpcZNbZm2ot_Aual9XrGB1MWjLrovZkMs,16749
 masster/spectrum.py,sha256=XJSUrqXZSzfpWnD8v5IMClXMRZLKLYIk014qaMOS9_k,49738
@@ -17,18 +17,18 @@ 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=mxUYBCBmkSBZB82557smSHCS25BAusuCewvW8zwsLGg,27130
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/adducts.py,sha256=jdtkkiMFeObRv3myluUx--IfpRsEq3-hPgkCb2VUxy4,32590
+masster/sample/adducts.py,sha256=S7meba3L1tSdjoDhkSiTI71H2NJLu4i1dtJwfDKWI1M,32591
 masster/sample/h5.py,sha256=B0gAmhrnoFoybotqsqiT8s-PkeZWUdIQfI-4cnM52Zc,115430
 masster/sample/helpers.py,sha256=JhzFpNh7j7YVUibIMuPQ50hBcGDEBCaBbmwA3Z5OhgM,41336
 masster/sample/lib.py,sha256=E-j9c3Wd8f9a-H8xj7CAOwlA8KcyXPoFyYm3c8r7LtI,33755
-masster/sample/load.py,sha256=TqBuDPrNgIotR-mL475AfDZntsW0JjYcy5AovVKRZxY,51560
+masster/sample/load.py,sha256=CSJnNfJ6EpWEIbDj92mJK0qFao0ycxuGf_w9DzWhlnY,51721
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
-masster/sample/plot.py,sha256=bQlEXCLQQWpUV88vGtftW9WAVwDKZ4k7TBirV9cO54w,82573
-masster/sample/processing.py,sha256=A1u5u7lGG0HR_ciUhJFmmwgugher7_AZQopNnbu65Bs,55910
+masster/sample/plot.py,sha256=0v4FzO_yzpUdATjdHZU4YO7UoW73Xlf51vVQByQ33X0,82574
+masster/sample/processing.py,sha256=Sh6IFxuFcmCspyizUPghd4Qqqk1mTPCNtvdxmyy0eKQ,55914
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=uQP5DLdsRSC2YwZZvspsL9rgl_HefB-oxrL2dpgg_fc,19788
+masster/sample/sample.py,sha256=_IUvUIlW2F4NRxsOdtBb1NePJJX_9FDcT5ZgM4O7ZRs,20534
 masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
-masster/sample/save.py,sha256=MfgHGiR2ofLyVp_rP9FIu7mUG3A6PEZHSscMypSTH7M,36425
+masster/sample/save.py,sha256=2yQtcQcRJjgAKPImTydj7LpyyMop_Q9JKRlNEK4yU6k,36339
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
 masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
 masster/sample/defaults/find_adducts_def.py,sha256=Bu2KiBJRxD0SAnOPNMm_Nk-6fx6QYoRXjFNGzz-0_o0,13570
@@ -37,17 +37,18 @@ masster/sample/defaults/find_ms2_def.py,sha256=KTELMAnioGLYbhzAwOgK14TZqboPEvzeB
 masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
 masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb5iMQL0iY,14579
 masster/study/__init__.py,sha256=55axdFuqRX4aXtJ8ocnhcLB32fNtmmJpCi58moO0r4g,237
-masster/study/export.py,sha256=CKrmje4_cQAJnQjQsB5u3mXkvDDbxKkAJO8e_MoeB38,59270
+masster/study/analysis.py,sha256=L-wXBnGZCLB5UUDrjIdOiMG9zdej3Tw_SftcEmmTukM,84264
+masster/study/export.py,sha256=Rp1vc5iDl-XFWo_RBVCJDGBNSKakq9f8aC2FeUCP9GA,59398
 masster/study/h5.py,sha256=eINlVmcJuntwbkkZHwzm10c63Kg7zib49vkzLDj1PyU,84790
-masster/study/helpers.py,sha256=6nDTNlsZbZWf9L6D5qzK2TUO2y7UBq51Ftj8N4bkIAk,160260
-masster/study/id.py,sha256=6NUBBKZCFOU1wlDKM0eXQeOIStSZCRNJ_3x7ZaIHzmM,55263
-masster/study/load.py,sha256=CQQY_7BzagE3oQTdDlqNyfuMdVWIAft-M4a2WCFnxp0,70695
-masster/study/merge.py,sha256=3R_Dg6l2mnJUu3gFVAgrAN5hFSQyfHbqYPmc2cUfJqQ,159232
-masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
-masster/study/plot.py,sha256=G9eStCUPxJTHrQk9TZpivk5rYxO1vbu5Yba6rP8NELM,90649
-masster/study/processing.py,sha256=WOcBdQ1agayASLkrtJ9GfUT0mgCJZVNnbuT77-J-KDY,52011
-masster/study/save.py,sha256=BANh9F1s-q7MclO1Mq_-v4xQyHeloEgmoPgRDVc-9aE,9037
-masster/study/study.py,sha256=rk-pJNg80N6xbROa9fqPfwVxFgzL_FLoSUNOTYeD5E0,40116
+masster/study/helpers.py,sha256=dU2YxAGPmu1w55mpcgNoHPpg2fNW-vK944aJy3YwLsU,163555
+masster/study/id.py,sha256=L5S0etAeEmtkzE06M32PNo3rp-WE01sLU6M5_TdNC3w,55266
+masster/study/load.py,sha256=x0OvfOoSY-6lQ8_B9KeDUh_E99eYRm1WGLnCY3CGqF8,71222
+masster/study/merge.py,sha256=MvvEwS2_UCWIrxROtuYTkJOu3pk8EasorbrfWug2e68,159736
+masster/study/parameters.py,sha256=bTvmcwX9INxzcrEAmTiFH8qeWVhwkvMTZjuP394pz5o,3279
+masster/study/plot.py,sha256=pAN5uQKYPUpupQVtKBloWjKOKpM_C9o2e3VWkJ-aZN8,102041
+masster/study/processing.py,sha256=hf8FEPONXz4x6G1fke6SEUnCJCv47cGeo--6h1c1Sis,56441
+masster/study/save.py,sha256=47AP518epJJ9TjaGGyrLKsMsyjIk8_J4ka7bmsnRtFQ,9268
+masster/study/study.py,sha256=YLt6tqCPkWvmKGBvhiyh1LeZgr165f9eqgiIV5OLomY,38393
 masster/study/study5_schema.json,sha256=ghBeAXFS4a4Uavdn6TUVs9GaR1QOTnADCjQTOkN0tjU,7563
 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
 masster/study/defaults/align_def.py,sha256=hHQbGgsOqMRHHr0Wn8Onr8XeaRz3-fFE0qGE-OMst80,20324
@@ -64,9 +65,9 @@ masster/study/defaults/study_def.py,sha256=h8dYbi9xv0sesCSQik49Z53IkskMmNtW6ixl7
 masster/wizard/README.md,sha256=mL1A3YWJZOefpJ6D0-HqGLkVRmUlOpwyVFdvJBeeoZM,14149
 masster/wizard/__init__.py,sha256=a2hcZnHASjfuw1lqZhZnvTR58rc33rRnoGAY_JfvGhI,683
 masster/wizard/example.py,sha256=xEZFTH9UZ8HKOm6s3JL8Js0Uw5ChnISWBHSZCL32vsM,7983
-masster/wizard/wizard.py,sha256=498u3rvYNC0mb0kDG7T71E8TKwMk2s1KKzHgDBn76c4,37698
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-masster-0.4.21.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.4.21.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.4.21.dist-info/RECORD,,
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+masster-0.5.0.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
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