masster 0.4.9__py3-none-any.whl → 0.4.11__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 (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/sample/sample5_schema.json CHANGED
@@ -1,95 +1,95 @@
1
1
  {
2
2
  "features_df": {
3
3
  "columns": {
4
- "adduct": {
5
- "dtype": "pl.Utf8"
6
- },
7
- "adduct_charge": {
8
- "dtype": "pl.Int64"
9
- },
10
- "adduct_group": {
4
+ "feature_uid": {
11
5
  "dtype": "pl.Int64"
12
6
  },
13
- "adduct_mass_neutral": {
14
- "dtype": "pl.Float64"
15
- },
16
- "adduct_mass_shift": {
17
- "dtype": "pl.Float64"
7
+ "feature_id": {
8
+ "dtype": "pl.Utf8"
18
9
  },
19
- "charge": {
10
+ "sample_uid": {
20
11
  "dtype": "pl.Int32"
21
12
  },
22
- "chrom": {
23
- "dtype": "pl.Object"
24
- },
25
- "chrom_area": {
13
+ "mz": {
26
14
  "dtype": "pl.Float64"
27
15
  },
28
- "chrom_coherence": {
16
+ "rt": {
29
17
  "dtype": "pl.Float64"
30
18
  },
31
- "chrom_height_scaled": {
19
+ "rt_original": {
32
20
  "dtype": "pl.Float64"
33
21
  },
34
- "chrom_prominence": {
22
+ "rt_start": {
35
23
  "dtype": "pl.Float64"
36
24
  },
37
- "chrom_prominence_scaled": {
25
+ "rt_end": {
38
26
  "dtype": "pl.Float64"
39
27
  },
40
- "feature_id": {
41
- "dtype": "pl.Utf8"
28
+ "rt_delta": {
29
+ "dtype": "pl.Float64"
42
30
  },
43
- "feature_uid": {
44
- "dtype": "pl.Int64"
31
+ "mz_start": {
32
+ "dtype": "pl.Float64"
45
33
  },
46
- "filled": {
47
- "dtype": "pl.Boolean"
34
+ "mz_end": {
35
+ "dtype": "pl.Float64"
48
36
  },
49
37
  "inty": {
50
38
  "dtype": "pl.Float64"
51
39
  },
40
+ "quality": {
41
+ "dtype": "pl.Float64"
42
+ },
43
+ "charge": {
44
+ "dtype": "pl.Int32"
45
+ },
52
46
  "iso": {
53
47
  "dtype": "pl.Int64"
54
48
  },
55
49
  "iso_of": {
56
50
  "dtype": "pl.Int64"
57
51
  },
58
- "ms2_scans": {
59
- "dtype": "pl.Object"
52
+ "adduct": {
53
+ "dtype": "pl.Utf8"
60
54
  },
61
- "ms2_specs": {
62
- "dtype": "pl.Object"
55
+ "adduct_charge": {
56
+ "dtype": "pl.Int64"
63
57
  },
64
- "mz": {
58
+ "adduct_mass_shift": {
65
59
  "dtype": "pl.Float64"
66
60
  },
67
- "mz_end": {
61
+ "adduct_mass_neutral": {
68
62
  "dtype": "pl.Float64"
69
63
  },
70
- "mz_start": {
71
- "dtype": "pl.Float64"
64
+ "adduct_group": {
65
+ "dtype": "pl.Int64"
72
66
  },
73
- "quality": {
74
- "dtype": "pl.Float64"
67
+ "chrom": {
68
+ "dtype": "pl.Object"
75
69
  },
76
- "rt": {
70
+ "filled": {
71
+ "dtype": "pl.Boolean"
72
+ },
73
+ "chrom_area": {
77
74
  "dtype": "pl.Float64"
78
75
  },
79
- "rt_delta": {
76
+ "chrom_coherence": {
80
77
  "dtype": "pl.Float64"
81
78
  },
82
- "rt_end": {
79
+ "chrom_prominence": {
83
80
  "dtype": "pl.Float64"
84
81
  },
85
- "rt_original": {
82
+ "chrom_prominence_scaled": {
86
83
  "dtype": "pl.Float64"
87
84
  },
88
- "rt_start": {
85
+ "chrom_height_scaled": {
89
86
  "dtype": "pl.Float64"
90
87
  },
91
- "sample_uid": {
92
- "dtype": "pl.Int32"
88
+ "ms2_scans": {
89
+ "dtype": "pl.Object"
90
+ },
91
+ "ms2_specs": {
92
+ "dtype": "pl.Object"
93
93
  }
94
94
  }
95
95
  },
masster/study/h5.py CHANGED
@@ -1686,19 +1686,6 @@ def _load_study5(self, filename=None):
1686
1686
  # Check if progress bar should be disabled based on log level
1687
1687
  tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
1688
1688
 
1689
- # Define loading steps for progress tracking
1690
- loading_steps = [
1691
- "metadata",
1692
- "samples_df",
1693
- "features_df",
1694
- "consensus_df",
1695
- "consensus_mapping_df",
1696
- "consensus_ms2",
1697
- ]
1698
-
1699
- # Check if progress bar should be disabled based on log level
1700
- tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
1701
-
1702
1689
  with h5py.File(filename, "r") as f:
1703
1690
  # Use progress bar to show loading progress
1704
1691
  with tqdm(
masster/study/helpers.py CHANGED
@@ -780,6 +780,7 @@ def _get_sample_uids(self, samples=None, seed=42):
780
780
  # choose a random sample of sample_uids
781
781
  if len(self.samples_df) > samples:
782
782
  np.random.seed(seed) # for reproducibility
783
+ self.logger.info(f"Randomly selected {samples} samples")
783
784
  return np.random.choice(
784
785
  self.samples_df["sample_uid"].to_list(),
785
786
  samples,