masster 0.4.0__py3-none-any.whl → 0.4.1__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.
Files changed (54) hide show
  1. masster/__init__.py +8 -8
  2. masster/_version.py +1 -1
  3. masster/chromatogram.py +3 -9
  4. masster/data/libs/README.md +1 -1
  5. masster/data/libs/ccm.csv +120 -120
  6. masster/data/libs/ccm.py +116 -62
  7. masster/data/libs/central_carbon_README.md +1 -1
  8. masster/data/libs/urine.py +161 -65
  9. masster/data/libs/urine_metabolites.csv +4693 -4693
  10. masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.mzML +2 -2
  11. masster/logger.py +43 -78
  12. masster/sample/__init__.py +1 -1
  13. masster/sample/adducts.py +264 -338
  14. masster/sample/defaults/find_adducts_def.py +8 -21
  15. masster/sample/defaults/find_features_def.py +1 -6
  16. masster/sample/defaults/get_spectrum_def.py +1 -5
  17. masster/sample/defaults/sample_def.py +1 -5
  18. masster/sample/h5.py +282 -561
  19. masster/sample/helpers.py +75 -131
  20. masster/sample/lib.py +17 -42
  21. masster/sample/load.py +17 -31
  22. masster/sample/parameters.py +2 -6
  23. masster/sample/plot.py +27 -88
  24. masster/sample/processing.py +87 -117
  25. masster/sample/quant.py +51 -57
  26. masster/sample/sample.py +90 -103
  27. masster/sample/sample5_schema.json +44 -44
  28. masster/sample/save.py +12 -35
  29. masster/sample/sciex.py +19 -66
  30. masster/spectrum.py +20 -58
  31. masster/study/__init__.py +1 -1
  32. masster/study/defaults/align_def.py +1 -5
  33. masster/study/defaults/fill_chrom_def.py +1 -5
  34. masster/study/defaults/fill_def.py +1 -5
  35. masster/study/defaults/integrate_chrom_def.py +1 -5
  36. masster/study/defaults/integrate_def.py +1 -5
  37. masster/study/defaults/study_def.py +25 -58
  38. masster/study/export.py +207 -233
  39. masster/study/h5.py +136 -470
  40. masster/study/helpers.py +202 -495
  41. masster/study/helpers_optimized.py +13 -40
  42. masster/study/id.py +110 -213
  43. masster/study/load.py +143 -230
  44. masster/study/plot.py +257 -518
  45. masster/study/processing.py +257 -469
  46. masster/study/save.py +5 -15
  47. masster/study/study.py +276 -379
  48. masster/study/study5_schema.json +96 -96
  49. {masster-0.4.0.dist-info → masster-0.4.1.dist-info}/METADATA +1 -1
  50. masster-0.4.1.dist-info/RECORD +67 -0
  51. masster-0.4.0.dist-info/RECORD +0 -67
  52. {masster-0.4.0.dist-info → masster-0.4.1.dist-info}/WHEEL +0 -0
  53. {masster-0.4.0.dist-info → masster-0.4.1.dist-info}/entry_points.txt +0 -0
  54. {masster-0.4.0.dist-info → masster-0.4.1.dist-info}/licenses/LICENSE +0 -0
masster/study/study5_schema.json CHANGED
@@ -1,43 +1,43 @@
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  {
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  "consensus_df": {
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  "columns": {
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- "adducts": {
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- "dtype": "pl.Object"
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+ "consensus_uid": {
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+ "dtype": "pl.Int64"
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  },
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- "bl": {
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- "dtype": "pl.Float64"
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+ "consensus_id": {
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+ "dtype": "pl.Utf8"
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  },
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- "charge_mean": {
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+ "quality": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_coherence_mean": {
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- "dtype": "pl.Float64"
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+ "number_samples": {
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+ "dtype": "pl.Int64"
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  },
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- "chrom_height_scaled_mean": {
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+ "rt": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_prominence_mean": {
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+ "mz": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_prominence_scaled_mean": {
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+ "rt_min": {
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  "dtype": "pl.Float64"
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  },
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- "consensus_id": {
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- "dtype": "pl.Utf8"
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+ "rt_max": {
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+ "dtype": "pl.Float64"
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  },
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- "consensus_uid": {
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- "dtype": "pl.Int64"
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+ "rt_mean": {
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+ "dtype": "pl.Float64"
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  },
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- "inty_mean": {
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+ "rt_start_mean": {
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  "dtype": "pl.Float64"
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  },
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- "iso_mean": {
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+ "rt_end_mean": {
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  "dtype": "pl.Float64"
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  },
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- "mz": {
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+ "rt_delta_mean": {
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  "dtype": "pl.Float64"
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  },
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- "mz_end_mean": {
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+ "mz_min": {
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  "dtype": "pl.Float64"
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  },
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  "mz_max": {
@@ -46,41 +46,41 @@
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  "mz_mean": {
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  "dtype": "pl.Float64"
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  },
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- "mz_min": {
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- "dtype": "pl.Float64"
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- },
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  "mz_start_mean": {
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  "dtype": "pl.Float64"
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  },
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- "number_ms2": {
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- "dtype": "pl.Int64"
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- },
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- "number_samples": {
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- "dtype": "pl.Int64"
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+ "mz_end_mean": {
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+ "dtype": "pl.Float64"
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  },
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- "quality": {
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+ "inty_mean": {
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  "dtype": "pl.Float64"
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  },
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- "rt": {
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+ "bl": {
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  "dtype": "pl.Float64"
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  },
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- "rt_delta_mean": {
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+ "chrom_coherence_mean": {
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  "dtype": "pl.Float64"
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  },
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- "rt_end_mean": {
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+ "chrom_prominence_mean": {
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  "dtype": "pl.Float64"
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  },
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- "rt_max": {
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+ "chrom_prominence_scaled_mean": {
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  "dtype": "pl.Float64"
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  },
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- "rt_mean": {
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+ "chrom_height_scaled_mean": {
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  "dtype": "pl.Float64"
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  },
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- "rt_min": {
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+ "iso_mean": {
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  "dtype": "pl.Float64"
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  },
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- "rt_start_mean": {
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+ "charge_mean": {
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  "dtype": "pl.Float64"
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+ },
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+ "number_ms2": {
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+ "dtype": "pl.Int64"
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+ },
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+ "adducts": {
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+ "dtype": "pl.Object"
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  }
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  }
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  },
@@ -133,137 +133,137 @@
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  },
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  "features_df": {
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  "columns": {
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- "adduct": {
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- "dtype": "pl.Utf8"
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- },
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- "adduct_charge": {
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- "dtype": "pl.Int64"
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- },
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- "adduct_group": {
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+ "feature_uid": {
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  "dtype": "pl.Int64"
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  },
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- "adduct_mass_neutral": {
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- "dtype": "pl.Float64"
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- },
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- "adduct_mass_shift": {
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- "dtype": "pl.Float64"
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+ "feature_id": {
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+ "dtype": "pl.Utf8"
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  },
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- "charge": {
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+ "sample_uid": {
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  "dtype": "pl.Int32"
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  },
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- "chrom": {
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- "dtype": "pl.Object"
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- },
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- "chrom_area": {
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+ "mz": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_coherence": {
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+ "rt": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_height_scaled": {
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+ "rt_original": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_prominence": {
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+ "rt_start": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_prominence_scaled": {
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+ "rt_end": {
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  "dtype": "pl.Float64"
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  },
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- "feature_id": {
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- "dtype": "pl.Utf8"
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+ "rt_delta": {
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+ "dtype": "pl.Float64"
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  },
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- "feature_uid": {
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- "dtype": "pl.Int64"
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+ "mz_start": {
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+ "dtype": "pl.Float64"
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  },
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- "filled": {
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- "dtype": "pl.Boolean"
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+ "mz_end": {
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+ "dtype": "pl.Float64"
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  },
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  "inty": {
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  "dtype": "pl.Float64"
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  },
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+ "quality": {
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+ "dtype": "pl.Float64"
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+ },
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+ "charge": {
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+ "dtype": "pl.Int32"
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+ },
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  "iso": {
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  "dtype": "pl.Int64"
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  },
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  "iso_of": {
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  "dtype": "pl.Int64"
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  },
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- "ms2_scans": {
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- "dtype": "pl.Object"
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+ "adduct": {
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+ "dtype": "pl.Utf8"
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  },
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- "ms2_specs": {
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- "dtype": "pl.Object"
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+ "adduct_charge": {
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+ "dtype": "pl.Int64"
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  },
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- "mz": {
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+ "adduct_mass_shift": {
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  "dtype": "pl.Float64"
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  },
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- "mz_end": {
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+ "adduct_mass_neutral": {
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  "dtype": "pl.Float64"
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  },
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- "mz_start": {
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- "dtype": "pl.Float64"
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+ "adduct_group": {
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+ "dtype": "pl.Int64"
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  },
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- "quality": {
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- "dtype": "pl.Float64"
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+ "chrom": {
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+ "dtype": "pl.Object"
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  },
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- "rt": {
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+ "filled": {
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+ "dtype": "pl.Boolean"
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+ },
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+ "chrom_area": {
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  "dtype": "pl.Float64"
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  },
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- "rt_delta": {
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+ "chrom_coherence": {
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  "dtype": "pl.Float64"
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  },
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- "rt_end": {
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+ "chrom_prominence": {
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  "dtype": "pl.Float64"
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  },
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- "rt_original": {
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+ "chrom_prominence_scaled": {
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  "dtype": "pl.Float64"
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  },
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- "rt_start": {
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+ "chrom_height_scaled": {
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  "dtype": "pl.Float64"
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  },
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- "sample_uid": {
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- "dtype": "pl.Int32"
220
+ "ms2_scans": {
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+ "dtype": "pl.Object"
222
+ },
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+ "ms2_specs": {
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+ "dtype": "pl.Object"
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  }
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  }
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  },
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  "samples_df": {
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  "columns": {
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- "map_id": {
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- "dtype": "pl.Int64"
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- },
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- "num_features": {
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- "dtype": "pl.Int64"
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- },
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- "num_ms1": {
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+ "sample_uid": {
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  "dtype": "pl.Int64"
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  },
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- "num_ms2": {
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+ "map_id": {
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  "dtype": "pl.Int64"
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  },
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- "sample_batch": {
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- "dtype": "pl.Int64"
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+ "sample_source": {
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+ "dtype": "pl.Utf8"
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  },
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- "sample_color": {
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+ "sample_name": {
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  "dtype": "pl.Utf8"
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  },
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- "sample_group": {
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+ "sample_path": {
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  "dtype": "pl.Utf8"
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  },
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- "sample_name": {
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+ "sample_type": {
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  "dtype": "pl.Utf8"
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  },
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- "sample_path": {
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+ "sample_group": {
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  "dtype": "pl.Utf8"
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  },
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+ "sample_batch": {
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+ "dtype": "pl.Int64"
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+ },
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  "sample_sequence": {
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  "dtype": "pl.Int64"
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  },
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- "sample_source": {
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+ "sample_color": {
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  "dtype": "pl.Utf8"
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  },
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- "sample_type": {
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- "dtype": "pl.Utf8"
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+ "num_features": {
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+ "dtype": "pl.Int64"
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  },
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- "sample_uid": {
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+ "num_ms1": {
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+ "dtype": "pl.Int64"
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+ },
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+ "num_ms2": {
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  "dtype": "pl.Int64"
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  }
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  }
{masster-0.4.0.dist-info → masster-0.4.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.4
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  Name: masster
3
- Version: 0.4.0
3
+ Version: 0.4.1
4
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  Summary: Mass spectrometry data analysis package
5
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  Project-URL: homepage, https://github.com/zamboni-lab/masster
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  Project-URL: repository, https://github.com/zamboni-lab/masster
masster-0.4.1.dist-info/RECORD ADDED
@@ -0,0 +1,67 @@
1
+ masster/__init__.py,sha256=8U4cIteNlYyHDrxWSbB_MsDKCX9tds07SJG8-vh8Oa8,738
2
+ masster/_version.py,sha256=uhkyzx8ZZ5g5UgWWNkUEm9tSwKYeno7iydu7-Yv4_7s,256
3
+ masster/chromatogram.py,sha256=NgPr1uLGJHjRu6PWZZGOrS3pCl7sye1yQCJjlRi9ZSY,19305
4
+ masster/logger.py,sha256=W50V_uh8RSYwGxDrDFhOuj5jpu2tKJyt_16lMw9kQwA,14755
5
+ masster/spectrum.py,sha256=7wKQes97sI-O2lxrkQnYuoroXFyAWgwSzS4TnjUX8RY,47710
6
+ masster/data/libs/README.md,sha256=bjODMSbzAcdKLUFB4tfC3a-yOo-oWwqBfONMMNDYES4,987
7
+ masster/data/libs/ccm.csv,sha256=Q6nylV1152uTpX-ydqWeGrc6L9kgv45xN_fBZ4f7Tvo,12754
8
+ masster/data/libs/ccm.py,sha256=TJPf7DxEhqKg0Xtu-brX_CIQQrTmUY1FQzzqL0SQx4I,20362
9
+ masster/data/libs/central_carbon_README.md,sha256=kse10ijMWdyGv02tK90zQhWzdN6hoXfEjzdezRptt2I,919
10
+ masster/data/libs/urine.py,sha256=0XOaygBMUsdXcCiV_MHwlIpI2fX6JT4iOUOx_bR6Kr4,10522
11
+ masster/data/libs/urine_metabolites.csv,sha256=98L11DolzWzAumTbtKdNNkpDbp-sNDzwAXypgqSZcik,653733
12
+ masster/data/libs/urine_metabolites.xml,sha256=9H60HoPd1gZLlSZnghftfjXPPpJwpHiAXBPar6G36J4,218706715
13
+ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.mzML,sha256=5KL8NfvSdUYGS_bKq-XmteT5S-CNOo2QA71XwpQVZ_k,40044432
14
+ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.sample5,sha256=fDiPJ6BoyzNN_-8kwEj2Xnjd0NcvKuJ1aDF8av0mQj8,30983576
15
+ 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
16
+ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
17
+ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan,sha256=ahi1Y3UhAj9Bj4Q2MlbgPekNdkJvMOoMXVOoR6CeIxc,13881220
18
+ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2,sha256=TFB0HW4Agkig6yht7FtgjUdbXax8jjKaHpSZSvuU5vs,3252224
19
+ masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
20
+ masster/sample/adducts.py,sha256=6LvMrrsFjvr4OCuNx6N9qCE1vlvRGEgXtmMz8iwMMQg,31675
21
+ masster/sample/h5.py,sha256=ZAGPJzPXkytmBOlpZXbyRM0K3buzxWd9f4a0hz85NMA,100475
22
+ masster/sample/helpers.py,sha256=m5soqGzQXxcL10tS_g_6MxTOtbnLoR9_e3CTvd1n25k,40591
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+ masster/sample/lib.py,sha256=abBEnHjItVCp_20qNT9xGdqBrKX4LL_4z4P6mNQuGRQ,33757
24
+ masster/sample/load.py,sha256=YCgMfv_0eIEdLv9KvNUwXCwGaJa1YZ5YpZCI6qmoUFU,50800
25
+ masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
26
+ masster/sample/plot.py,sha256=ynF4xNs2QPIYGButT-HkrofbYZPeLtyBXo15AOJKH7M,82783
27
+ masster/sample/processing.py,sha256=GBRUk-u17P_KpgpuHuVBYq0PDs-Y0IeP1jblIFkDa7s,49264
28
+ masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
29
+ masster/sample/sample.py,sha256=C27jbAsn7zWFnL2MLTh4vCtkECQoZgl0jyerCqEslYI,18173
30
+ masster/sample/sample5_schema.json,sha256=voVB6z0TaIJwU-_SPUEYWKH7mKC16ycTe1nW6gODYP8,3916
31
+ masster/sample/save.py,sha256=Mc6buxdLJQevEyPSpuMB65rqsEGc4YtdiTiRIP3hrc0,31950
32
+ masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
33
+ masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
34
+ masster/sample/defaults/find_adducts_def.py,sha256=OKINCF9k6AoSFVXfRJNC9U9c2XVva2YVcX0AkDAICW0,13380
35
+ masster/sample/defaults/find_features_def.py,sha256=Bcd39uav1BniwKgrsB-I1maF3ljf4Wb1f5yv0pDYfts,17745
36
+ masster/sample/defaults/find_ms2_def.py,sha256=KTELMAnioGLYbhzAwOgK14TZqboPEvzeBN0HC-v0Z5A,9872
37
+ masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
38
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