masster 0.4.9__py3-none-any.whl → 0.4.11__py3-none-any.whl

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Files changed (13) hide show
  1. masster/_version.py +1 -1
  2. masster/lib/__init__.py +9 -0
  3. masster/lib/lib.py +598 -0
  4. masster/sample/sample5_schema.json +44 -44
  5. masster/study/h5.py +0 -13
  6. masster/study/helpers.py +1 -0
  7. masster/study/plot.py +136 -289
  8. masster/study/study5_schema.json +149 -149
  9. {masster-0.4.9.dist-info → masster-0.4.11.dist-info}/METADATA +1 -1
  10. {masster-0.4.9.dist-info → masster-0.4.11.dist-info}/RECORD +13 -11
  11. {masster-0.4.9.dist-info → masster-0.4.11.dist-info}/WHEEL +0 -0
  12. {masster-0.4.9.dist-info → masster-0.4.11.dist-info}/entry_points.txt +0 -0
  13. {masster-0.4.9.dist-info → masster-0.4.11.dist-info}/licenses/LICENSE +0 -0
masster/study/study5_schema.json CHANGED
@@ -1,104 +1,104 @@
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  {
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  "consensus_df": {
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  "columns": {
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- "adduct_charge_top": {
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+ "consensus_uid": {
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  "dtype": "pl.Int64"
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  },
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- "adduct_group": {
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+ "consensus_id": {
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+ "dtype": "pl.Utf8"
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+ },
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+ "quality": {
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+ "dtype": "pl.Float64"
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+ },
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+ "number_samples": {
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  "dtype": "pl.Int64"
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  },
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- "adduct_mass_neutral_top": {
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+ "rt": {
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  "dtype": "pl.Float64"
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  },
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- "adduct_mass_shift_top": {
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+ "mz": {
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  "dtype": "pl.Float64"
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  },
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- "adduct_of": {
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- "dtype": "pl.Int64"
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+ "rt_min": {
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+ "dtype": "pl.Float64"
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  },
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- "adduct_top": {
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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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- "adducts": {
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- "dtype": "pl.Object"
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+ "rt_mean": {
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+ "dtype": "pl.Float64"
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  },
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- "bl": {
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+ "rt_start_mean": {
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  "dtype": "pl.Float64"
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  },
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- "charge_mean": {
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+ "rt_end_mean": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_coherence_mean": {
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+ "rt_delta_mean": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_height_scaled_mean": {
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+ "mz_min": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_prominence_mean": {
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+ "mz_max": {
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  "dtype": "pl.Float64"
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  },
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- "chrom_prominence_scaled_mean": {
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+ "mz_mean": {
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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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+ "mz_start_mean": {
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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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+ "mz_end_mean": {
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+ "dtype": "pl.Float64"
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  },
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  "inty_mean": {
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  "dtype": "pl.Float64"
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  },
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- "iso_mean": {
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+ "bl": {
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  "dtype": "pl.Float64"
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  },
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- "mz": {
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+ "chrom_coherence_mean": {
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  "dtype": "pl.Float64"
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  },
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- "mz_end_mean": {
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+ "chrom_prominence_mean": {
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  "dtype": "pl.Float64"
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  },
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- "mz_max": {
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+ "chrom_prominence_scaled_mean": {
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  "dtype": "pl.Float64"
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  },
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- "mz_mean": {
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+ "chrom_height_scaled_mean": {
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  "dtype": "pl.Float64"
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  },
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- "mz_min": {
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+ "iso_mean": {
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  "dtype": "pl.Float64"
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  },
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- "mz_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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- "number_samples": {
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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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- },
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- "rt": {
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- "dtype": "pl.Float64"
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+ "adducts": {
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+ "dtype": "pl.Object"
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  },
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- "rt_delta_mean": {
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- "dtype": "pl.Float64"
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+ "adduct_charge_top": {
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+ "dtype": "pl.Int64"
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  },
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- "rt_end_mean": {
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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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- "rt_max": {
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+ "adduct_mass_neutral_top": {
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  "dtype": "pl.Float64"
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  },
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- "rt_mean": {
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+ "adduct_mass_shift_top": {
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  "dtype": "pl.Float64"
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  },
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- "rt_min": {
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- "dtype": "pl.Float64"
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+ "adduct_of": {
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+ "dtype": "pl.Int64"
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  },
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- "rt_start_mean": {
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- "dtype": "pl.Float64"
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+ "adduct_top": {
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+ "dtype": "pl.Utf8"
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  }
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  }
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  },
@@ -151,135 +151,156 @@
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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"
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+ "ms2_scans": {
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+ "dtype": "pl.Object"
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+ },
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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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- "id_df": {
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+ "samples_df": {
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  "columns": {
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- "consensus_uid": {
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+ "sample_uid": {
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  "dtype": "pl.Int64"
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  },
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- "lib_uid": {
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+ "map_id": {
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  "dtype": "pl.Int64"
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  },
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- "matcher": {
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- "dtype": "pl.String"
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+ "sample_source": {
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+ "dtype": "pl.Utf8"
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  },
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- "mz_delta": {
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- "dtype": "pl.Float64"
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+ "sample_name": {
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+ "dtype": "pl.Utf8"
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  },
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- "rt_delta": {
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- "dtype": "pl.Null"
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+ "sample_path": {
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+ "dtype": "pl.Utf8"
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  },
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- "score": {
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- "dtype": "pl.Float64"
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+ "sample_type": {
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+ "dtype": "pl.Utf8"
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+ },
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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_color": {
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+ "dtype": "pl.Utf8"
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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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+ "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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  }
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  },
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  "lib_df": {
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  "columns": {
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- "adduct": {
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- "dtype": "pl.String"
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+ "lib_uid": {
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+ "dtype": "pl.Int64"
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  },
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  "cmpd_uid": {
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  "dtype": "pl.Int64"
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  },
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- "db": {
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- "dtype": "pl.String"
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+ "source_id": {
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+ "dtype": "pl.Null"
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  },
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- "db_id": {
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+ "name": {
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  "dtype": "pl.String"
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  },
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- "formula": {
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+ "smiles": {
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  "dtype": "pl.String"
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  },
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  "inchi": {
@@ -288,72 +309,51 @@
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  "inchikey": {
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  "dtype": "pl.String"
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  },
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- "lib_uid": {
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- "dtype": "pl.Int64"
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+ "formula": {
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+ "dtype": "pl.String"
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+ },
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+ "adduct": {
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+ "dtype": "pl.String"
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  },
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  "m": {
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  "dtype": "pl.Float64"
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  },
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+ "z": {
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+ "dtype": "pl.Int64"
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+ },
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  "mz": {
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  "dtype": "pl.Float64"
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  },
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- "name": {
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- "dtype": "pl.String"
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- },
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  "rt": {
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  "dtype": "pl.Null"
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  },
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- "smiles": {
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+ "db_id": {
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  "dtype": "pl.String"
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  },
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- "source_id": {
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- "dtype": "pl.Null"
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- },
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- "z": {
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- "dtype": "pl.Int64"
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+ "db": {
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+ "dtype": "pl.String"
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  }
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  }
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  },
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- "samples_df": {
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+ "id_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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- "dtype": "pl.Int64"
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- },
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- "num_ms2": {
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+ "consensus_uid": {
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  "dtype": "pl.Int64"
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  },
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- "sample_batch": {
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+ "lib_uid": {
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  "dtype": "pl.Int64"
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  },
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- "sample_color": {
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- "dtype": "pl.Utf8"
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- },
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- "sample_group": {
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- "dtype": "pl.Utf8"
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- },
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- "sample_name": {
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- "dtype": "pl.Utf8"
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- },
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- "sample_path": {
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- "dtype": "pl.Utf8"
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- },
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- "sample_sequence": {
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- "dtype": "pl.Int64"
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+ "mz_delta": {
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+ "dtype": "pl.Float64"
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  },
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- "sample_source": {
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- "dtype": "pl.Utf8"
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+ "rt_delta": {
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+ "dtype": "pl.Null"
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  },
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- "sample_type": {
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- "dtype": "pl.Utf8"
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+ "matcher": {
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+ "dtype": "pl.String"
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  },
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- "sample_uid": {
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- "dtype": "pl.Int64"
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+ "score": {
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+ "dtype": "pl.Float64"
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  }
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  }
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  }
{masster-0.4.9.dist-info → masster-0.4.11.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
2
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  Name: masster
3
- Version: 0.4.9
3
+ Version: 0.4.11
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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-0.4.9.dist-info → masster-0.4.11.dist-info}/RECORD RENAMED
@@ -1,5 +1,5 @@
1
1
  masster/__init__.py,sha256=8U4cIteNlYyHDrxWSbB_MsDKCX9tds07SJG8-vh8Oa8,738
2
- masster/_version.py,sha256=0yrEn9iWdV_opaqa2Sq9St0gGLqdVLUjTS0SKr3szC0,256
2
+ masster/_version.py,sha256=Ra822EfcCSSsug6aojKBn4P__-I2P5hLd9y2DnUcJqg,257
3
3
  masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
4
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  masster/logger.py,sha256=W50V_uh8RSYwGxDrDFhOuj5jpu2tKJyt_16lMw9kQwA,14755
5
5
  masster/spectrum.py,sha256=_upC_g2N9gwTaflXAugs9pSXpKUmzbIehofDordk7WI,47718
@@ -14,6 +14,8 @@ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecR
14
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  masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
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  masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan,sha256=ahi1Y3UhAj9Bj4Q2MlbgPekNdkJvMOoMXVOoR6CeIxc,13881220
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  masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2,sha256=TFB0HW4Agkig6yht7FtgjUdbXax8jjKaHpSZSvuU5vs,3252224
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+ masster/lib/__init__.py,sha256=TcePNx3SYZHz6763TL9Sg4gUNXaRWjlrOtyS6vsu-hg,178
18
+ masster/lib/lib.py,sha256=seAOqzat74iF6YnbNakU3rF5MN5t9WABIpcIPTvU1q8,24987
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  masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
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  masster/sample/adducts.py,sha256=jdtkkiMFeObRv3myluUx--IfpRsEq3-hPgkCb2VUxy4,32590
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  masster/sample/h5.py,sha256=7NJeErlIHwC2Qh3nchusLZJWjBGue9zExAx08C89qhg,111889
@@ -25,7 +27,7 @@ masster/sample/plot.py,sha256=abLnG0Bk75vqSGQz6uA3uTK3IE9N-s687ZH-n8Mhdzg,82757
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  masster/sample/processing.py,sha256=lCHRv290oAFOxe_zR5GMi4FdxodjJh1rj2uLWy_wHnc,49771
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  masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
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  masster/sample/sample.py,sha256=WH4G9tG2AjXAWv_tK08X4R2peaDlXTKqXTq2V4-P6rE,18353
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- masster/sample/sample5_schema.json,sha256=EKHVKXhqMqsavO34A4AJLPpysW0s2iLuLwjeTJP9R_8,3916
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+ masster/sample/sample5_schema.json,sha256=voVB6z0TaIJwU-_SPUEYWKH7mKC16ycTe1nW6gODYP8,3916
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  masster/sample/save.py,sha256=XZl5ITYdOjojYFOoUZ-0ygVSPH1kT5Va6e8NyuTRNAI,32500
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  masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
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  masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
@@ -36,16 +38,16 @@ masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2At
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  masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb5iMQL0iY,14579
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  masster/study/__init__.py,sha256=Zspv6U8jFqjkHGYdNdDy1rfUnCSolCzUdgSSg98PRgE,166
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  masster/study/export.py,sha256=L-YOUGSgVeTprYnrQxaN0qC8MRqUdDQ0D4o2h7HLi2Q,54813
39
- masster/study/h5.py,sha256=j9LJT_BtK_TIJB552r5Rhpw7Clg9mZxzp6vxJ4X44kE,84063
40
- masster/study/helpers.py,sha256=ggY97l-spkXFaceEYy4D6ndcWZaD4aPnPcKOb9T7R8I,160208
41
+ masster/study/h5.py,sha256=Sbde1cxAAIq0EjNiTxQgJgHHVKFw29q510YBJRa_egw,83691
42
+ masster/study/helpers.py,sha256=TS1x9sMlcUPhEqGcPgDnzd84XqbUkJkf770iAUcI8RQ,160278
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  masster/study/id.py,sha256=EOw-2dM8nnx8QcQF1qAFfGqql75JusONuDBjmAuMU2w,44723
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  masster/study/load.py,sha256=tK3ueWxrauyveZukyh1YaV8h8fSFDytLnTmrEpFvcwU,70458
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  masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
44
- masster/study/plot.py,sha256=VBj1seZGGDJ9KGw8pmjuitn5H_tck1IPWSduWk57m3s,93855
46
+ masster/study/plot.py,sha256=c_VxZxupGi7UYx2r4b2XR-SWRefLuo8s8zbIoVg0PgE,86876
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  masster/study/processing.py,sha256=JlIstxo9mdqudl30yI-Wd-Ru9AfAeiwBPmqaW-dTl54,73867
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  masster/study/save.py,sha256=F_H34zmvxV54Ds64ju90JJLy_F4hg6nRdHhJ9ssWKLA,6704
47
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  masster/study/study.py,sha256=k097_YaYykhtkI6Ykcr5QCcFvo1eBLWXWLKycrid51w,34846
48
- masster/study/study5_schema.json,sha256=06cB473eo_IzzbsT1Q9W4-svNTdgNJhCS86NVpuyySI,7246
50
+ masster/study/study5_schema.json,sha256=vZIaGfcPJmhy_6pDEweKF7nEYrHwmV4_uxbGLcYfK30,7246
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  masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
50
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  masster/study/defaults/align_def.py,sha256=hHQbGgsOqMRHHr0Wn8Onr8XeaRz3-fFE0qGE-OMst80,20324
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  masster/study/defaults/export_def.py,sha256=eXl3h4aoLX88XkHTpqahLd-QZ2gjUqrmjq8IJULXeWo,1203
@@ -58,8 +60,8 @@ masster/study/defaults/integrate_chrom_def.py,sha256=0MNIWGTjty-Zu-NTQsIweuj3UVq
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  masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
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  masster/study/defaults/merge_def.py,sha256=EBsKE3hsAkTEzN9dpdRD5W3_suTKy_WZ_96rwS0uBuE,8572
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  masster/study/defaults/study_def.py,sha256=h8dYbi9xv0sesCSQik49Z53IkskMmNtW6ixl7it5pL0,16033
61
- masster-0.4.9.dist-info/METADATA,sha256=ulvm1pAw0IpOdNsTvgm00orsh9G4Y2V5tRUhEmLxKes,44188
62
- masster-0.4.9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
63
- masster-0.4.9.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
64
- masster-0.4.9.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
65
- masster-0.4.9.dist-info/RECORD,,
63
+ masster-0.4.11.dist-info/METADATA,sha256=d-0v4eIqBo_LJNbnSN-6FncgNRMX_a1enOjueLtPGTs,44189
64
+ masster-0.4.11.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
65
+ masster-0.4.11.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
66
+ masster-0.4.11.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
67
+ masster-0.4.11.dist-info/RECORD,,