masster 0.5.22__py3-none-any.whl → 0.5.24__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of masster might be problematic. Click here for more details.

Files changed (37) hide show
  1. masster/_version.py +1 -1
  2. masster/logger.py +35 -19
  3. masster/sample/adducts.py +15 -29
  4. masster/sample/defaults/find_adducts_def.py +1 -3
  5. masster/sample/defaults/sample_def.py +4 -4
  6. masster/sample/h5.py +203 -361
  7. masster/sample/helpers.py +14 -30
  8. masster/sample/lib.py +3 -3
  9. masster/sample/load.py +21 -29
  10. masster/sample/plot.py +222 -132
  11. masster/sample/processing.py +42 -55
  12. masster/sample/sample.py +37 -46
  13. masster/sample/save.py +37 -61
  14. masster/sample/sciex.py +13 -11
  15. masster/sample/thermo.py +69 -74
  16. masster/spectrum.py +15 -15
  17. masster/study/analysis.py +650 -586
  18. masster/study/defaults/identify_def.py +1 -3
  19. masster/study/defaults/merge_def.py +6 -7
  20. masster/study/defaults/study_def.py +1 -5
  21. masster/study/export.py +35 -96
  22. masster/study/h5.py +134 -211
  23. masster/study/helpers.py +385 -459
  24. masster/study/id.py +239 -290
  25. masster/study/importers.py +84 -93
  26. masster/study/load.py +159 -178
  27. masster/study/merge.py +1112 -1098
  28. masster/study/plot.py +195 -149
  29. masster/study/processing.py +144 -191
  30. masster/study/save.py +14 -13
  31. masster/study/study.py +89 -130
  32. masster/wizard/wizard.py +764 -714
  33. {masster-0.5.22.dist-info → masster-0.5.24.dist-info}/METADATA +27 -1
  34. {masster-0.5.22.dist-info → masster-0.5.24.dist-info}/RECORD +37 -37
  35. {masster-0.5.22.dist-info → masster-0.5.24.dist-info}/WHEEL +0 -0
  36. {masster-0.5.22.dist-info → masster-0.5.24.dist-info}/entry_points.txt +0 -0
  37. {masster-0.5.22.dist-info → masster-0.5.24.dist-info}/licenses/LICENSE +0 -0
{masster-0.5.22.dist-info → masster-0.5.24.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: masster
3
- Version: 0.5.22
3
+ Version: 0.5.24
4
4
  Summary: Mass spectrometry data analysis package
5
5
  Project-URL: homepage, https://github.com/zamboni-lab/masster
6
6
  Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -727,6 +727,8 @@ Requires-Dist: pytest>=7.0.0; extra == 'test'
727
727
  Description-Content-Type: text/markdown
728
728
 
729
729
  # MASSter
730
+ [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/masster)](https://badge.fury.io/py/masster)
731
+ [![PyPI version](https://badge.fury.io/py/masster.svg)](https://badge.fury.io/py/masster)
730
732
 
731
733
  **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.
732
734
 
@@ -823,6 +825,30 @@ study.plot_samples_umap()
823
825
  study.plot_samples_2d()
824
826
  ```
825
827
 
828
+ ### Quick Start with Wizard
829
+ MASSter includes a Wizard to automatically process everything:
830
+
831
+ ```python
832
+ from masster import Wizard
833
+
834
+ # Create wizard instance
835
+ wiz = Wizard(source="./raw_data",
836
+ folder="./output",
837
+ num_cores=8)
838
+
839
+ # Generate analysis scripts
840
+ wiz.create_scripts()
841
+
842
+ # Test with single file, then run full batch
843
+ wiz.test_and_run()
844
+ ```
845
+
846
+ ### One-Line Command Processing
847
+ Or, from the command-line:
848
+ ```bash
849
+ 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()"
850
+ ```
851
+
826
852
  ## License
827
853
  GNU Affero General Public License v3
828
854
 
{masster-0.5.22.dist-info → masster-0.5.24.dist-info}/RECORD RENAMED
@@ -1,8 +1,8 @@
1
1
  masster/__init__.py,sha256=B7zftzdElF2Wb5B7KvkD6TONnMIY-Jxeen3s49dgmzs,1029
2
- masster/_version.py,sha256=4HOjpCuCuNY78DZ2P_GWL7HWMcoGK_P8IwMz9LKoTq0,257
2
+ masster/_version.py,sha256=koihKimRza_kbnrpmX9DP_9ctG8yI80eHbJh5pY2xPs,257
3
3
  masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
4
- masster/logger.py,sha256=XT2gUcUIct8LWzTp9n484g5MaB89toT76CGA41oBvfA,18375
5
- masster/spectrum.py,sha256=TWIgDcl0lveG40cLVZTWGp8-FxMolu-P8EjZyRBtXL4,49850
4
+ masster/logger.py,sha256=oHEFPH1LzBHbmeP9WFaRZCWyqd14GasJjZMLI8a4O3I,19439
5
+ masster/spectrum.py,sha256=LlmxrI5MFS3aPrGSdqUSKVY0rJnKeBh3Frdh6a4dPvA,49722
6
6
  masster/data/libs/aa.csv,sha256=Sja1DyMsiaM2NfLcct4kAAcXYwPCukJJW8sDkup9w_c,1924
7
7
  masster/data/libs/ccm.csv,sha256=Q6nylV1152uTpX-ydqWeGrc6L9kgv45xN_fBZ4f7Tvo,12754
8
8
  masster/data/libs/urine.csv,sha256=iRrR4N8Wzb8KDhHJA4LqoQC35pp93FSaOKvXPrgFHis,653736
@@ -13,40 +13,40 @@ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecR
13
13
  masster/lib/__init__.py,sha256=TcePNx3SYZHz6763TL9Sg4gUNXaRWjlrOtyS6vsu-hg,178
14
14
  masster/lib/lib.py,sha256=SGWuiCTHc65khmLndC2cFBCO1rk8-SS6BkG4C_nOf-o,44984
15
15
  masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
16
- masster/sample/adducts.py,sha256=SU6S3pyyLQUSg6yPcdj3p4MfwNDsp0_FYwYYb7F4li0,33798
17
- masster/sample/h5.py,sha256=0FE6eH9n8RaO59HjKnFo0kKmr8L44UOQIBqcpD3LW0s,117749
18
- masster/sample/helpers.py,sha256=Mt9LX-Dy1Xro1a_Sy6nxQzCkP_-q7nK4xVnNm44v7UA,43872
19
- masster/sample/lib.py,sha256=jrzqvglaCGzZQSSRXEQXYSJ_UTaFMdpSQbWiZd1DJyc,33976
20
- masster/sample/load.py,sha256=GP8oYICEqHdog9_sFPiBJVwdy7foavVF7g1ffZ729-s,48711
16
+ masster/sample/adducts.py,sha256=ALUSeY8fDf4oWl-g1wEffBDRk_apKTDwd_FOdxtP5Es,33511
17
+ masster/sample/h5.py,sha256=uEbsfaMgRWgADLhw3j6rdXjHqRz4bmLQKjAzXXGA12M,109285
18
+ masster/sample/helpers.py,sha256=opitF12aS3KNfwM0GFwiITX129AAi0HXvEW32oljTL4,43627
19
+ masster/sample/lib.py,sha256=YIeG9nBiSMllu3xkqcQXnMe6pXJ9sJSN7un8SORgVJ4,33968
20
+ masster/sample/load.py,sha256=tpPqRZtmfOY1AibHBBqcYfPD8SoI8Uue-IiDOA20DYc,48402
21
21
  masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
22
- masster/sample/plot.py,sha256=5qn2Cpl363f3hW1ZeI4BZV9_36VLx39PKQMrebJhfp4,104864
23
- masster/sample/processing.py,sha256=iPbkC2yxBZZfDkXb4xl12qeu0Z1qwm0VLQfk3bQq33w,56322
22
+ masster/sample/plot.py,sha256=fQWWG-BeJz3XdtIVYTlV1_mM5xqZw5cYjQEmJU68t2U,105244
23
+ masster/sample/processing.py,sha256=7FmlDO_vsVbUfI62QSoHXKkgGtfjMLHLRdvaB4KdmP4,56018
24
24
  masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
25
- masster/sample/sample.py,sha256=Khhjcd1okZBxVM6bOvGV4ZU-FUagiqgZjkWm3afhECs,22365
25
+ masster/sample/sample.py,sha256=-xliZfE_6I0tRkMZa8yChiMtdbKXdLnF4xnD-LtIgZY,22078
26
26
  masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
27
- masster/sample/save.py,sha256=pbiRoWEA2DnhDKmMJncjveNlBqizJLOVRm5cug4ZwyM,38658
28
- masster/sample/sciex.py,sha256=1jwy40Ime4wPWiyfGHVnlaY8Q8dkHdQ9aGafvumdYoI,21771
29
- masster/sample/thermo.py,sha256=X5yDVWroHOFkWvugezrcCV5ZKPVcpTX5VKEvFSJK1vU,28128
27
+ masster/sample/save.py,sha256=RD3tRoTNy2ANKoU-oZSfu47nQ4ATSAB-Io2EN0RUZaI,37994
28
+ masster/sample/sciex.py,sha256=jzMrw5iKzbCFVgmgbU65eIr10eegzKng9WKx1Inl8Dg,21740
29
+ masster/sample/thermo.py,sha256=zcH4aZg2hQnZp9rM618ZUiQXRuUqFRmVFdbCg0SnIOQ,27775
30
30
  masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
31
- masster/sample/defaults/find_adducts_def.py,sha256=Bu2KiBJRxD0SAnOPNMm_Nk-6fx6QYoRXjFNGzz-0_o0,13570
31
+ masster/sample/defaults/find_adducts_def.py,sha256=bK05FcACdj0t-T8x6zWUbCzxRxbR7P0u8o8U23RIFrc,13552
32
32
  masster/sample/defaults/find_features_def.py,sha256=Bcd39uav1BniwKgrsB-I1maF3ljf4Wb1f5yv0pDYfts,17745
33
33
  masster/sample/defaults/find_ms2_def.py,sha256=mr_XtzlhYfXt7kYWVFPt1ReGqHZQDPXe-1pGND2VvV8,9844
34
34
  masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
35
- masster/sample/defaults/sample_def.py,sha256=XJPtQPqgkpaLEng3eqBPznCwcKVPJSw3FC6wNVcEu5E,15460
35
+ masster/sample/defaults/sample_def.py,sha256=MWWeEexGG2Ahbs-id4uq2doIgH-Ja96GioXaSl2CxN8,15449
36
36
  masster/study/__init__.py,sha256=55axdFuqRX4aXtJ8ocnhcLB32fNtmmJpCi58moO0r4g,237
37
- masster/study/analysis.py,sha256=L-wXBnGZCLB5UUDrjIdOiMG9zdej3Tw_SftcEmmTukM,84264
38
- masster/study/export.py,sha256=c1HJdLAM6Ply0n8f0DjMk4mXd9lOYePr60UJTBksUho,60092
39
- masster/study/h5.py,sha256=bznE9kKEfLNo0QtbyC6a6snfnR3Zjkx5BcjBNbRVlJ8,99579
40
- masster/study/helpers.py,sha256=FdvQV-CgQyBhXMqk6_92aKSBsZhJBK4joLxEdKzmuhw,192011
41
- masster/study/id.py,sha256=H6LhD0fbuxM4i0JIhHvWKLMa86fpXyEAHzbCCW5ffBA,91288
42
- masster/study/importers.py,sha256=1Oco0yMid_siMMZdK7rQlhS20XikgjBBNAirbTHx5O8,13958
43
- masster/study/load.py,sha256=EsKpxUuduu-w1TREfHTYxRdEncWTd15h2IwoB3D_nuc,72070
44
- masster/study/merge.py,sha256=SwrsbcoI6hIuepvTJEFNoXncwMx1XXr6FVOvkSyfIbs,169239
37
+ masster/study/analysis.py,sha256=bf2o_ywvwdPz1mZAHPETCPjWbvhoL9eEl1rLaz46Rp4,82032
38
+ masster/study/export.py,sha256=63xP7pPBNsrAKWZP6XnqAyWO4lEfqtqKfO0SafNvzyg,58871
39
+ masster/study/h5.py,sha256=gJRWNQxBTyFKD3qRmEbM24YZ-HdyUk-veYgwQbK0eoE,99104
40
+ masster/study/helpers.py,sha256=pRcVvGmm6NX-GEvWfYZXZjGc_C0WyklqSQx1PdpYn2E,189694
41
+ masster/study/id.py,sha256=dTMNdBE7eOQZdFSU0KZwd7vFpqOmNlQnLI0VGW98y8w,89570
42
+ masster/study/importers.py,sha256=iOe9w6uEn39ShosRms8n_zIrsSBczb51CAMoMrxSUw4,13587
43
+ masster/study/load.py,sha256=-qz9tAVYzI5is7_-z43FndcJJk95BmuMUOIxYzZoO_I,71314
44
+ masster/study/merge.py,sha256=FEya_v2cMNvzNBtxzTv57KxfwNxT1R63LDrvnYIHORY,164557
45
45
  masster/study/parameters.py,sha256=bTvmcwX9INxzcrEAmTiFH8qeWVhwkvMTZjuP394pz5o,3279
46
- masster/study/plot.py,sha256=RXuTlL-jpdLn9aRrxNvTrRU8Zr4504pia-BEWYzpSfY,114048
47
- masster/study/processing.py,sha256=5b8K4tP-Xu1-mhdf0om-m-g65Z9Uz3Dp4UBhuMLh0yU,58627
48
- masster/study/save.py,sha256=47AP518epJJ9TjaGGyrLKsMsyjIk8_J4ka7bmsnRtFQ,9268
49
- masster/study/study.py,sha256=Qt1ltc20LRjPvfuwHLX3AGszNAzZG3t7oM0GbS6Ixbc,38891
46
+ masster/study/plot.py,sha256=HIz8GMxN988KDXP425cpYohCgrgMrMCWBQ2s5ncmLoI,113816
47
+ masster/study/processing.py,sha256=oQGepG5-AXP9GGk8NTzl_i1ztgDp3TPwE2x15BmnpMw,57353
48
+ masster/study/save.py,sha256=tF00anwwQDe2qxumv_4AP_1UOo0-f28Tkd2WXGyNHbI,9182
49
+ masster/study/study.py,sha256=_IL6pCw29JI0p2ujdaMr_gsfaFkq3PFWO5NPuLpshYA,37867
50
50
  masster/study/study5_schema.json,sha256=uLA9TIb5loki87_BEdwSNyPYahwOanacYisXdIK0_Z0,8044
51
51
  masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
52
52
  masster/study/defaults/align_def.py,sha256=Du0F592ej2einT8kOx8EUs610axSvur8_-6N19O-uJY,10209
@@ -54,15 +54,15 @@ masster/study/defaults/export_def.py,sha256=eXl3h4aoLX88XkHTpqahLd-QZ2gjUqrmjq8I
54
54
  masster/study/defaults/fill_def.py,sha256=pdH-lwknaMqnB_lXdGmeSqk9KgLMoOgNlp82eEunx6U,9124
55
55
  masster/study/defaults/find_consensus_def.py,sha256=2KRRMsCDP7pwNrLCC6eI5uQgMXqiNdiI6pSvxNJ8L5M,8598
56
56
  masster/study/defaults/find_ms2_def.py,sha256=RL0DFG41wQ05U8UQKUGr3vzSl3mU0m0knQus8DpSoJE,5070
57
- masster/study/defaults/identify_def.py,sha256=96rxoCAPQj_yX-3mRoD2LTkTLJgG27eJQqwarLv5jL0,10580
57
+ masster/study/defaults/identify_def.py,sha256=nFj-pv6q1eRgSgoRr78YEnqulPPMWo2Ju5HbYlpD9xo,10548
58
58
  masster/study/defaults/integrate_chrom_def.py,sha256=0MNIWGTjty-Zu-NTQsIweuj3UVqEY3x1x8pK0mPwYak,7264
59
59
  masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
60
- masster/study/defaults/merge_def.py,sha256=krR099IkENLlJVxpSjdje3E6h-_qtlc3Ep6Hpy6inrU,12978
61
- masster/study/defaults/study_def.py,sha256=h8dYbi9xv0sesCSQik49Z53IkskMmNtW6ixl7it5pL0,16033
60
+ masster/study/defaults/merge_def.py,sha256=99TJtIk7mSoq8NMJMJ4b-cy7gUUixQN69krxttBnkfA,12899
61
+ masster/study/defaults/study_def.py,sha256=xXOAcb8hez0woWwA1_T3fcokjiLJkq3hwA3OS6elb6I,15965
62
62
  masster/wizard/__init__.py,sha256=L9G_datyGSFJjrBVklEVpZVLGXzUhDiWobtiygBH8vQ,669
63
- masster/wizard/wizard.py,sha256=aTNVhYoMK5B1uR2zrdbwEyZX-Zd86e4sUGhkQ2bgiDo,65352
64
- masster-0.5.22.dist-info/METADATA,sha256=tLbIWPgMewKVqyz7MSbwLZZY5JOPUaEfYMx-q5w4rkk,45153
65
- masster-0.5.22.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
66
- masster-0.5.22.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
67
- masster-0.5.22.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
68
- masster-0.5.22.dist-info/RECORD,,
63
+ masster/wizard/wizard.py,sha256=11utDrZSt7R8D16Sl-NbRKHcgzhQEu8gW_q2V02-Qi0,66483
64
+ masster-0.5.24.dist-info/METADATA,sha256=QH2sJUX_6eW2B9eTFg7T7G--9WTbTqzsrT_UQxxPSs0,45970
65
+ masster-0.5.24.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
66
+ masster-0.5.24.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
67
+ masster-0.5.24.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
68
+ masster-0.5.24.dist-info/RECORD,,