Merge pull request #290 from monarch-initiative/288-fixing-param-name…

…-in-semsim-to-exomiserdb-utils-cli-command

 Fixing param name in semsim-to-exomiserdb utils cli command

src/pheval/analyse/disease_prioritisation_analysis.py

@@ -170,16 +170,20 @@ def assess_disease_prioritisation(
                     disease_match = self._record_matched_disease(
                         disease, rank_stats, standardised_disease_result
                     )
-                    relevant_ranks.append(
-                        disease_match.rank
-                    ) if disease_match else relevant_ranks.append(0)
+                    (
+                        relevant_ranks.append(disease_match.rank)
+                        if disease_match
+                        else relevant_ranks.append(0)
+                    )
                     break
             PrioritisationRankRecorder(
                 rank_stats.total,
                 self.results_dir,
-                DiseasePrioritisationResult(self.phenopacket_path, disease)
-                if disease_match is None
-                else disease_match,
+                (
+                    DiseasePrioritisationResult(self.phenopacket_path, disease)
+                    if disease_match is None
+                    else disease_match
+                ),
                 rank_records,
             ).record_rank()
         rank_stats.relevant_result_ranks.append(relevant_ranks)

src/pheval/analyse/gene_prioritisation_analysis.py

@@ -161,16 +161,20 @@ def assess_gene_prioritisation(self, rank_stats: RankStats, rank_records: defaul
                     gene_match = self._record_matched_gene(
                         gene, rank_stats, standardised_gene_result
                     )
-                    relevant_ranks.append(gene_match.rank) if gene_match else relevant_ranks.append(
-                        0
+                    (
+                        relevant_ranks.append(gene_match.rank)
+                        if gene_match
+                        else relevant_ranks.append(0)
                     )
                     break
             PrioritisationRankRecorder(
                 rank_stats.total,
                 self.results_dir,
-                GenePrioritisationResult(self.phenopacket_path, gene.gene_symbol)
-                if gene_match is None
-                else gene_match,
+                (
+                    GenePrioritisationResult(self.phenopacket_path, gene.gene_symbol)
+                    if gene_match is None
+                    else gene_match
+                ),
                 rank_records,
             ).record_rank()
         rank_stats.relevant_result_ranks.append(relevant_ranks)

src/pheval/analyse/variant_prioritisation_analysis.py

@@ -164,16 +164,20 @@ def assess_variant_prioritisation(
                 )
                 if variant == result_variant:
                     variant_match = self._record_matched_variant(rank_stats, result)
-                    relevant_ranks.append(
-                        variant_match.rank
-                    ) if variant_match else relevant_ranks.append(0)
+                    (
+                        relevant_ranks.append(variant_match.rank)
+                        if variant_match
+                        else relevant_ranks.append(0)
+                    )
                     break
             PrioritisationRankRecorder(
                 rank_stats.total,
                 self.results_dir,
-                VariantPrioritisationResult(self.phenopacket_path, variant)
-                if variant_match is None
-                else variant_match,
+                (
+                    VariantPrioritisationResult(self.phenopacket_path, variant)
+                    if variant_match is None
+                    else variant_match
+                ),
                 rank_records,
             ).record_rank()
         rank_stats.relevant_result_ranks.append(relevant_ranks)

src/pheval/cli.py

@@ -1,4 +1,5 @@
 """PhEval CLI Module """
+
 import logging
 
 import click

src/pheval/cli_pheval.py

@@ -1,6 +1,7 @@
 """
 Monarch Initiative
 """
+
 from pathlib import Path
 
 import click

src/pheval/implementations/__init__.py

@@ -1,4 +1,5 @@
 """implementations"""
+
 from functools import cache
 
 from class_resolver import ClassResolver

src/pheval/prepare/create_spiked_vcf.py

@@ -279,9 +279,11 @@ def construct_variant_entry(self, proband_variant_data: ProbandCausativeVariant)
             str(proband_variant_data.variant.pos),
             ".",
             proband_variant_data.variant.ref,
-            f"<{proband_variant_data.variant.alt}>"
-            if proband_variant_data.variant.ref == "N"
-            else proband_variant_data.variant.alt,
+            (
+                f"<{proband_variant_data.variant.alt}>"
+                if proband_variant_data.variant.ref == "N"
+                else proband_variant_data.variant.alt
+            ),
             "100",
             "PASS",
             proband_variant_data.info if proband_variant_data.info else ".",

src/pheval/runners/runner.py

@@ -1,4 +1,5 @@
 """Runners Module"""
+
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from datetime import datetime

src/pheval/utils/docs_gen.py

@@ -1,4 +1,5 @@
 """docs generate utils"""
+
 import ast
 import os
 import shutil

src/pheval/utils/phenopacket_utils.py

@@ -301,12 +301,16 @@ def _diagnosis_from_interpretations(self) -> List[ProbandDisease]:
         diagnoses = []
         interpretation = self.interpretations()
         for i in interpretation:
-            diagnoses.append(
-                ProbandDisease(
-                    disease_name=i.diagnosis.disease.label,
-                    disease_identifier=i.diagnosis.disease.id,
+            (
+                diagnoses.append(
+                    ProbandDisease(
+                        disease_name=i.diagnosis.disease.label,
+                        disease_identifier=i.diagnosis.disease.id,
+                    )
                 )
-            ) if i.diagnosis.disease.label != "" and i.diagnosis.disease.id != "" else None
+                if i.diagnosis.disease.label != "" and i.diagnosis.disease.id != ""
+                else None
+            )
         return diagnoses
 
     def _diagnosis_from_disease(self) -> List[ProbandDisease]:

src/pheval/utils/semsim_utils.py

@@ -1,6 +1,7 @@
 """
 Contains all pheval utility methods
 """
+
 from pathlib import Path
 
 import numpy

src/pheval/utils/utils.py

@@ -1,4 +1,5 @@
 """Contains all pheval utility methods"""
+
 import logging
 import random
 from pathlib import Path

tests/test_cli.py

@@ -1,4 +1,5 @@
 """CLI Test """
+
 import logging
 import shutil
 import tempfile