pheval 0.5.4__tar.gz → 0.5.5__tar.gz

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  1. {pheval-0.5.4 → pheval-0.5.5}/PKG-INFO +1 -1
  2. {pheval-0.5.4 → pheval-0.5.5}/pyproject.toml +1 -1
  3. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/rank_stats.py +13 -37
  4. {pheval-0.5.4 → pheval-0.5.5}/LICENSE +0 -0
  5. {pheval-0.5.4 → pheval-0.5.5}/README.md +0 -0
  6. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/__init__.py +0 -0
  7. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/__init__.py +0 -0
  8. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/benchmark.py +0 -0
  9. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/benchmark_db_manager.py +0 -0
  10. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/benchmark_output_type.py +0 -0
  11. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/binary_classification_curves.py +0 -0
  12. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/binary_classification_stats.py +0 -0
  13. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/generate_plots.py +0 -0
  14. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/generate_rank_comparisons.py +0 -0
  15. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/analyse/run_data_parser.py +0 -0
  16. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/cli.py +0 -0
  17. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/cli_pheval.py +0 -0
  18. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/cli_pheval_utils.py +0 -0
  19. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/config_parser.py +0 -0
  20. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/implementations/__init__.py +0 -0
  21. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/infra/__init__.py +0 -0
  22. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/infra/exomiserdb.py +0 -0
  23. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/post_processing/__init__.py +0 -0
  24. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/post_processing/phenopacket_truth_set.py +0 -0
  25. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/post_processing/post_processing.py +0 -0
  26. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/post_processing/validate_result_format.py +0 -0
  27. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/prepare/__init__.py +0 -0
  28. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/prepare/create_noisy_phenopackets.py +0 -0
  29. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/prepare/create_spiked_vcf.py +0 -0
  30. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/prepare/custom_exceptions.py +0 -0
  31. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/prepare/prepare_corpus.py +0 -0
  32. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/prepare/update_phenopacket.py +0 -0
  33. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/resources/alternate_ouputs/CADA_results.txt +0 -0
  34. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/resources/alternate_ouputs/DeepPVP_results.txt +0 -0
  35. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/resources/alternate_ouputs/OVA_results.txt +0 -0
  36. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/resources/alternate_ouputs/Phen2Gene_results.json +0 -0
  37. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/resources/alternate_ouputs/Phenolyzer_results.txt +0 -0
  38. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/resources/alternate_ouputs/lirical_results.tsv +0 -0
  39. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/resources/alternate_ouputs/svanna_results.tsv +0 -0
  40. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/resources/hgnc_complete_set.txt +0 -0
  41. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/run_metadata.py +0 -0
  42. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/runners/__init__.py +0 -0
  43. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/runners/runner.py +0 -0
  44. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/__init__.py +0 -0
  45. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/docs_gen.py +0 -0
  46. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/docs_gen.sh +0 -0
  47. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/exomiser.py +0 -0
  48. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/file_utils.py +0 -0
  49. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/logger.py +0 -0
  50. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/phenopacket_utils.py +0 -0
  51. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/semsim_utils.py +0 -0
  52. {pheval-0.5.4 → pheval-0.5.5}/src/pheval/utils/utils.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: pheval
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- Version: 0.5.4
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+ Version: 0.5.5
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  Summary:
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  Author: Yasemin Bridges
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  Author-email: y.bridges@qmul.ac.uk
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "pheval"
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- version = "0.5.4"
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+ version = "0.5.5"
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  description = ""
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  authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
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  "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",
@@ -124,24 +124,11 @@ class Ranks:
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  return np.mean(precision_at_k)
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  @classmethod
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- def mean_average_precision_at_k(cls, df: pl.LazyFrame, k: int) -> pl.LazyFrame:
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- """
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- Compute Mean Average Precision at K (MAP@K) by averaging AP@K scores.
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- Args:
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- df (pl.LazyFrame): The dataframe calculate MAP@K for each query.
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- k (int): The upper rank limit.
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- Returns:
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- pl.LazyFrame: The dataframe with MAP@K for each query.
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- """
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+ def mean_average_precision_at_k(cls, df: pl.LazyFrame, k: int) -> float:
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  ap_at_k_df = cls._average_precision_at_k(df, k)
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- return (
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- ap_at_k_df.select(
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- pl.col(f"ap@{k}").sum() / df.select(Ranks.NUMBER_OF_SAMPLES).collect()
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- )
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- .fill_null(0.0)
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- .collect()
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- .item()
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- )
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+ ap_sum = ap_at_k_df.select(pl.col(f"ap@{k}").sum()).collect().item()
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+ num_samples = df.select(Ranks.NUMBER_OF_SAMPLES).collect().item()
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+ return ap_sum / num_samples
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  @classmethod
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  def _calculate_ndcg_at_k(cls, ranks: List[int], k: int) -> float:
@@ -165,29 +152,18 @@ class Ranks:
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  )
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153
 
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  @classmethod
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- def mean_normalised_discounted_cumulative_gain(cls, df: pl.LazyFrame, k: int) -> pl.Float64:
169
- """
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- Compute mean normalised discounted cumulative gain.
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- Args:
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- df (pl.LazyFrame): The dataframe to calculate mean normalised cumulative gain.
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- k (int): The upper rank limit.
174
- Returns:
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- pl.LazyFrame: The dataframe with mean normalised cumulative gain.
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- """
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+ def mean_normalised_discounted_cumulative_gain(cls, df: pl.LazyFrame, k: int) -> float:
177
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  filtered_df = cls._filter_results(df, k)
178
- return (
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- filtered_df.with_columns(
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- pl.struct("ranks")
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- .map_elements(
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- lambda row: cls._calculate_ndcg_at_k(row["ranks"], k), return_dtype=pl.Float64
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- )
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- .alias(f"NDCG@{k}")
157
+ ndcg_df = filtered_df.with_columns(
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+ pl.struct("ranks")
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+ .map_elements(
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+ lambda row: cls._calculate_ndcg_at_k(row["ranks"], k), return_dtype=pl.Float64
185
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  )
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- .select(pl.col(f"NDCG@{k}").sum() / df.select(Ranks.NUMBER_OF_SAMPLES).collect())
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- .fill_null(0.0)
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- .collect()
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- .item()
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+ .alias(f"NDCG@{k}")
190
163
  )
164
+ ndcg_sum = ndcg_df.select(pl.col(f"NDCG@{k}").sum()).collect().item()
165
+ num_samples = df.select(Ranks.NUMBER_OF_SAMPLES).collect().item()
166
+ return ndcg_sum / num_samples
191
167
 
192
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193
169
  def compute_rank_stats(run_identifier: str, result_scan: pl.LazyFrame) -> pl.LazyFrame:
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