pheval 0.3.6__py3-none-any.whl → 0.3.7__py3-none-any.whl

pheval/analyse/disease_prioritisation_analysis.py

@@ -10,11 +10,7 @@ from pheval.analyse.prioritisation_result_types import DiseasePrioritisationResu
 from pheval.analyse.rank_stats import RankStats
 from pheval.analyse.run_data_parser import TrackInputOutputDirectories
 from pheval.post_processing.post_processing import RankedPhEvalDiseaseResult
-from pheval.utils.file_utils import (
-    all_files,
-    files_with_suffix,
-    obtain_phenopacket_path_from_pheval_result,
-)
+from pheval.utils.file_utils import all_files
 from pheval.utils.phenopacket_utils import PhenopacketUtil, ProbandDisease, phenopacket_reader
 
 
@@ -217,7 +213,7 @@ def _obtain_causative_diseases(phenopacket_path: Path) -> List[ProbandDisease]:
 
 
 def assess_phenopacket_disease_prioritisation(
-    standardised_disease_result: Path,
+    phenopacket_path: Path,
     score_order: str,
     results_dir_and_input: TrackInputOutputDirectories,
     threshold: float,
@@ -230,7 +226,7 @@ def assess_phenopacket_disease_prioritisation(
     against the recorded causative diseases for a proband in the Phenopacket.
 
     Args:
-        standardised_disease_result (Path): Path to the PhEval standardised disease result file.
+        phenopacket_path (Path): Path to the Phenopacket.
         score_order (str): The order in which scores are arranged, either ascending or descending.
         results_dir_and_input (TrackInputOutputDirectories): Input and output directories.
         threshold (float): Threshold for assessment.
@@ -238,8 +234,8 @@ def assess_phenopacket_disease_prioritisation(
         disease_rank_comparison (defaultdict): Default dictionary for disease rank comparisons.
         disease_binary_classification_stats (BinaryClassificationStats): BinaryClassificationStats class instance.
     """
-    phenopacket_path = obtain_phenopacket_path_from_pheval_result(
-        standardised_disease_result, all_files(results_dir_and_input.phenopacket_dir)
+    standardised_disease_result = results_dir_and_input.results_dir.joinpath(
+        f"pheval_disease_results/{phenopacket_path.stem}-pheval_disease_result.tsv"
     )
     pheval_disease_result = read_standardised_result(standardised_disease_result)
     proband_diseases = _obtain_causative_diseases(phenopacket_path)
@@ -276,12 +272,9 @@ def benchmark_disease_prioritisation(
     """
     disease_rank_stats = RankStats()
     disease_binary_classification_stats = BinaryClassificationStats()
-    for standardised_result in files_with_suffix(
-        results_directory_and_input.results_dir.joinpath("pheval_disease_results/"),
-        ".tsv",
-    ):
+    for phenopacket_path in all_files(results_directory_and_input.phenopacket_dir):
         assess_phenopacket_disease_prioritisation(
-            standardised_result,
+            phenopacket_path,
             score_order,
             results_directory_and_input,
             threshold,

pheval/analyse/gene_prioritisation_analysis.py

@@ -10,11 +10,7 @@ from pheval.analyse.prioritisation_result_types import GenePrioritisationResult
 from pheval.analyse.rank_stats import RankStats
 from pheval.analyse.run_data_parser import TrackInputOutputDirectories
 from pheval.post_processing.post_processing import RankedPhEvalGeneResult
-from pheval.utils.file_utils import (
-    all_files,
-    files_with_suffix,
-    obtain_phenopacket_path_from_pheval_result,
-)
+from pheval.utils.file_utils import all_files
 from pheval.utils.phenopacket_utils import PhenopacketUtil, ProbandCausativeGene, phenopacket_reader
 
 
@@ -209,7 +205,7 @@ def _obtain_causative_genes(phenopacket_path: Path) -> List[ProbandCausativeGene
 
 
 def assess_phenopacket_gene_prioritisation(
-    standardised_gene_result: Path,
+    phenopacket_path: Path,
     score_order: str,
     results_dir_and_input: TrackInputOutputDirectories,
     threshold: float,
@@ -222,7 +218,7 @@ def assess_phenopacket_gene_prioritisation(
     against the recorded causative genes for a proband in the Phenopacket.
 
     Args:
-        standardised_gene_result (Path): Path to the PhEval standardised gene result file.
+        phenopacket_path (Path): Path to the Phenopacket.
         score_order (str): The order in which scores are arranged, either ascending or descending.
         results_dir_and_input (TrackInputOutputDirectories): Input and output directories.
         threshold (float): Threshold for assessment.
@@ -230,8 +226,8 @@ def assess_phenopacket_gene_prioritisation(
         gene_rank_comparison (defaultdict): Default dictionary for gene rank comparisons.
         gene_binary_classification_stats (BinaryClassificationStats): BinaryClassificationStats class instance.
     """
-    phenopacket_path = obtain_phenopacket_path_from_pheval_result(
-        standardised_gene_result, all_files(results_dir_and_input.phenopacket_dir)
+    standardised_gene_result = results_dir_and_input.results_dir.joinpath(
+        f"pheval_gene_results/{phenopacket_path.stem}-pheval_gene_result.tsv"
     )
     pheval_gene_result = read_standardised_result(standardised_gene_result)
     proband_causative_genes = _obtain_causative_genes(phenopacket_path)
@@ -266,11 +262,9 @@ def benchmark_gene_prioritisation(
     """
     gene_rank_stats = RankStats()
     gene_binary_classification_stats = BinaryClassificationStats()
-    for standardised_result in files_with_suffix(
-        results_directory_and_input.results_dir.joinpath("pheval_gene_results/"), ".tsv"
-    ):
+    for phenopacket_path in all_files(results_directory_and_input.phenopacket_dir):
         assess_phenopacket_gene_prioritisation(
-            standardised_result,
+            phenopacket_path,
             score_order,
             results_directory_and_input,
             threshold,

pheval/analyse/parse_pheval_result.py

@@ -1,3 +1,4 @@
+import logging
 from pathlib import Path
 from typing import List
 
@@ -5,6 +6,8 @@ import pandas as pd
 
 from pheval.post_processing.post_processing import PhEvalResult
 
+info_log = logging.getLogger("info")
+
 
 def read_standardised_result(standardised_result_path: Path) -> List[dict]:
     """
@@ -16,7 +19,11 @@ def read_standardised_result(standardised_result_path: Path) -> List[dict]:
     Returns:
         List[dict]: A list of dictionaries representing the content of the standardised result file.
     """
-    return pd.read_csv(standardised_result_path, delimiter="\t").to_dict("records")
+    if standardised_result_path.is_file():
+        return pd.read_csv(standardised_result_path, delimiter="\t").to_dict("records")
+    else:
+        info_log.info(f"Could not find {standardised_result_path}")
+        return pd.DataFrame().to_dict("records")
 
 
 def parse_pheval_result(

pheval/analyse/variant_prioritisation_analysis.py

@@ -10,11 +10,7 @@ from pheval.analyse.prioritisation_result_types import VariantPrioritisationResu
 from pheval.analyse.rank_stats import RankStats
 from pheval.analyse.run_data_parser import TrackInputOutputDirectories
 from pheval.post_processing.post_processing import RankedPhEvalVariantResult
-from pheval.utils.file_utils import (
-    all_files,
-    files_with_suffix,
-    obtain_phenopacket_path_from_pheval_result,
-)
+from pheval.utils.file_utils import all_files
 from pheval.utils.phenopacket_utils import GenomicVariant, PhenopacketUtil, phenopacket_reader
 
 
@@ -211,7 +207,7 @@ def _obtain_causative_variants(phenopacket_path: Path) -> List[GenomicVariant]:
 
 
 def assess_phenopacket_variant_prioritisation(
-    standardised_variant_result: Path,
+    phenopacket_path: Path,
     score_order: str,
     results_dir_and_input: TrackInputOutputDirectories,
     threshold: float,
@@ -224,7 +220,7 @@ def assess_phenopacket_variant_prioritisation(
     against the recorded causative variants for a proband in the Phenopacket.
 
     Args:
-        standardised_variant_result (Path): Path to the PhEval standardised variant result file.
+        phenopacket_path (Path): Path to the Phenopacket.
         score_order (str): The order in which scores are arranged, either ascending or descending.
         results_dir_and_input (TrackInputOutputDirectories): Input and output directories.
         threshold (float): Threshold for assessment.
@@ -232,10 +228,10 @@ def assess_phenopacket_variant_prioritisation(
         variant_rank_comparison (defaultdict): Default dictionary for variant rank comparisons.
         variant_binary_classification_stats (BinaryClassificationStats): BinaryClassificationStats class instance.
     """
-    phenopacket_path = obtain_phenopacket_path_from_pheval_result(
-        standardised_variant_result, all_files(results_dir_and_input.phenopacket_dir)
-    )
     proband_causative_variants = _obtain_causative_variants(phenopacket_path)
+    standardised_variant_result = results_dir_and_input.results_dir.joinpath(
+        f"pheval_variant_results/{phenopacket_path.stem}-pheval_variant_result.tsv"
+    )
     pheval_variant_result = read_standardised_result(standardised_variant_result)
     AssessVariantPrioritisation(
         phenopacket_path,
@@ -270,12 +266,9 @@ def benchmark_variant_prioritisation(
     """
     variant_rank_stats = RankStats()
     variant_binary_classification_stats = BinaryClassificationStats()
-    for standardised_result in files_with_suffix(
-        results_directory_and_input.results_dir.joinpath("pheval_variant_results/"),
-        ".tsv",
-    ):
+    for phenopacket_path in all_files(results_directory_and_input.phenopacket_dir):
         assess_phenopacket_variant_prioritisation(
-            standardised_result,
+            phenopacket_path,
             score_order,
             results_directory_and_input,
             threshold,

pheval/post_processing/post_processing.py

@@ -375,11 +375,11 @@ def generate_pheval_result(
         info_log.warning(f"No results found for {tool_result_path.name}")
         return
     ranked_pheval_result = _create_pheval_result(pheval_result, sort_order_str)
-    if all(isinstance(result, RankedPhEvalGeneResult) for result in ranked_pheval_result):
+    if all(isinstance(result, PhEvalGeneResult) for result in pheval_result):
         _write_pheval_gene_result(ranked_pheval_result, output_dir, tool_result_path)
-    elif all(isinstance(result, RankedPhEvalVariantResult) for result in ranked_pheval_result):
+    elif all(isinstance(result, PhEvalVariantResult) for result in pheval_result):
         _write_pheval_variant_result(ranked_pheval_result, output_dir, tool_result_path)
-    elif all(isinstance(result, RankedPhEvalDiseaseResult) for result in ranked_pheval_result):
+    elif all(isinstance(result, PhEvalDiseaseResult) for result in pheval_result):
         _write_pheval_disease_result(ranked_pheval_result, output_dir, tool_result_path)
     else:
         raise ValueError("Results are not all of the same type.")

pheval/utils/file_utils.py

@@ -70,35 +70,6 @@ def normalise_file_name(file_path: Path) -> str:
     return re.sub("[\u0300-\u036f]", "", normalised_file_name)
 
 
-def obtain_phenopacket_path_from_pheval_result(
-    pheval_result_path: Path, phenopacket_paths: list[Path]
-) -> Path:
-    """
-    Obtains the phenopacket file name when given a pheval result file name
-    and a list of full paths of phenopackets to be queried.
-
-    Args:
-        pheval_result_path (Path): The PhEval result.
-        phenopacket_paths (list[Path]): List of full paths of phenopackets to be queried.
-
-    Returns:
-        Path: The matching phenopacket file path from the provided list.
-    """
-    pheval_result_path_stem_stripped = pheval_result_path.stem.split("-pheval_")[0]
-    matching_phenopacket_paths = [
-        phenopacket_path
-        for phenopacket_path in phenopacket_paths
-        if phenopacket_path.stem == pheval_result_path_stem_stripped
-    ]
-    if matching_phenopacket_paths:
-        return matching_phenopacket_paths[0]
-    else:
-        raise FileNotFoundError(
-            f"Unable to find matching phenopacket file named "
-            f"{pheval_result_path_stem_stripped}.json for {pheval_result_path.name}"
-        )
-
-
 def ensure_file_exists(*files: str):
     """Ensures the existence of files passed as parameter
     Raises:

{pheval-0.3.6.dist-info → pheval-0.3.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pheval
-Version: 0.3.6
+Version: 0.3.7
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk

{pheval-0.3.6.dist-info → pheval-0.3.7.dist-info}/RECORD

@@ -4,17 +4,17 @@ pheval/analyse/analysis.py,sha256=ponm3P8nvzJNmcrNZ2_KudEhWSaWshd_Gd30D-aau8s,77
 pheval/analyse/benchmark_generator.py,sha256=AeuwbaPb4j_dyBGPRgEBxQk2NahDb5u4xHyFiqp5Fes,5943
 pheval/analyse/benchmarking_data.py,sha256=aNZkWdmWemlnC1Tg35MtR60S9YC71QWS2rMuzkUc3w0,768
 pheval/analyse/binary_classification_stats.py,sha256=E35YjvGM-zFnuEt8M3pgN03vBab4MH6ih726QKvuogg,12519
-pheval/analyse/disease_prioritisation_analysis.py,sha256=qadEVhBMtBgtjGCJLhNQA510F8Pd0Ll4NAQXoT23BYs,12649
-pheval/analyse/gene_prioritisation_analysis.py,sha256=lAN171xfXqweK8ie6191s_6WPPGjZKJXL1Z0dIqp54k,12373
+pheval/analyse/disease_prioritisation_analysis.py,sha256=mGfGYF5Eu7LxyBkAy6xMG1nDURaPiJY4rRQyKDcQe-4,12451
+pheval/analyse/gene_prioritisation_analysis.py,sha256=KSEQV6EvqtWESmO4Zc3Q9CwrjoMzxRiFUDKuAVvQtuM,12190
 pheval/analyse/generate_plots.py,sha256=MFORnFTgoelYAahFlu3Dc3Rul4cwCg8Bloxe62vONSc,21350
 pheval/analyse/generate_summary_outputs.py,sha256=s9pXMSW6xm4ZBe1aCd0UJSaFiKBvpUfPwJ2BI4qfTas,6591
 pheval/analyse/parse_benchmark_summary.py,sha256=Y8uPTlHTEiaeVBOqxMcdOqjY3ZBtOS3DoRycL78Dzxg,2384
-pheval/analyse/parse_pheval_result.py,sha256=j8YFVA0YXfySOkm8gMwrfIuV45DI9AX3ETn7h-r8ayE,1211
+pheval/analyse/parse_pheval_result.py,sha256=2-J_c90KSs49EDjMukl8dgQyWJ0lZMlF-9ZYzD9hWzg,1438
 pheval/analyse/prioritisation_rank_recorder.py,sha256=EVe8DoEvvp0_WMAcjfVxmDGGRFPEELi7hEVjH3sIpLY,3223
 pheval/analyse/prioritisation_result_types.py,sha256=qJoB6O-lFYmzAMcTQeDJZQNLJ6hleoKDYATTkhvFF98,1228
 pheval/analyse/rank_stats.py,sha256=knj1tsKrly17QgtOUVpqA14UjbO99N3ydkWN4xU6c2k,15785
 pheval/analyse/run_data_parser.py,sha256=HzBKsJL2skjmrRZdrF3VYzswtKNgbX6U5qhY_kqq9mA,1552
-pheval/analyse/variant_prioritisation_analysis.py,sha256=ApmUeTW0cl_BPh7LusbApxtgjEXEkhuNFyh0DxKKpgU,12384
+pheval/analyse/variant_prioritisation_analysis.py,sha256=eF3SIvU6MNv1KR8ZmwXvTF4IoNu2qfwaBHA0uKZ8uMc,12186
 pheval/cli.py,sha256=X4tDi7e3VB3v2RawkqIbfv4SFPCBuQwMXMnYCPTGtIo,1570
 pheval/cli_pheval.py,sha256=fWbKUcPTZZSa1EJEtH_lNn1XE6qRApRHihqUZS5owrA,2424
 pheval/cli_pheval_utils.py,sha256=kySsSa7NyewwVwYBMu93y8l5_qSJaVkdXklGchcXExU,20504
@@ -24,7 +24,7 @@ pheval/implementations/__init__.py,sha256=BMUTotjTdgy5j5xubWCIQgRXrSQ1ZIcjooer7r
 pheval/infra/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval/infra/exomiserdb.py,sha256=pM9-TfjrgurtH4OtM1Enk5oVhIxGQN3rKRlrxHuObTM,5080
 pheval/post_processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pheval/post_processing/post_processing.py,sha256=tjdk-LKj5TORwGDKNzEiLViy9oMRLVR9hG1b7E8RfkI,13368
+pheval/post_processing/post_processing.py,sha256=Xzcrb7I0DiLBT3tp0oM8_L8Ld64fTgRHBstQuNSrFHk,13329
 pheval/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval/prepare/create_noisy_phenopackets.py,sha256=UbBRWDD95BFHPv03VYx04v35AGwJ9ynLltYKqQJHbZ0,11236
 pheval/prepare/create_spiked_vcf.py,sha256=A_nIAhoU48nAeocpIu5UE41db4oBGj2cSoT-U-3qQ1Q,21111
@@ -46,12 +46,12 @@ pheval/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval/utils/docs_gen.py,sha256=6FGtHicBC0rZKi0tdL3Epsg8d4osE44I9f1Ga0j4JLA,3193
 pheval/utils/docs_gen.sh,sha256=LyKLKjaZuf4UJ962CWfM-XqkxtvM8O2N9wHZS5mcb9A,477
 pheval/utils/exomiser.py,sha256=m2u0PH2z9lFPaB3LVkZCmPmH5e55q1NoTzNl46zRRP8,683
-pheval/utils/file_utils.py,sha256=9HoCmtF73D3wY6bBhFLefMBI5uhvCe_meZeHXQzF_ts,4640
+pheval/utils/file_utils.py,sha256=m21cz-qjDYqnI8ClUv3J9fKizex98a-9bSEerQ75i_c,3576
 pheval/utils/phenopacket_utils.py,sha256=4inrnhZ4UjYgO0Y85ls_Nxq6voAIIXQV57_fMeIX-24,26792
 pheval/utils/semsim_utils.py,sha256=s7ZCR2VfPYnOh7ApX6rv66eGoVSm9QJaVYOWBEhlXpo,6151
 pheval/utils/utils.py,sha256=9V6vCT8l1g4O2-ZATYqsVyd7AYZdWGd-Ksy7_oIC3eE,2343
-pheval-0.3.6.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-pheval-0.3.6.dist-info/METADATA,sha256=VC-lX9dK2KZUkh91WuDK4ygdu6tTw3WSBRkrVe-EZJ0,1810
-pheval-0.3.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pheval-0.3.6.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
-pheval-0.3.6.dist-info/RECORD,,
+pheval-0.3.7.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+pheval-0.3.7.dist-info/METADATA,sha256=BwicFNwmR9Hm8o2YxBJUJvrIeGwAevFFk-DT2pm07S4,1810
+pheval-0.3.7.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pheval-0.3.7.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
+pheval-0.3.7.dist-info/RECORD,,