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186 generalise rankcomparisongenerator class #192

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merged 3 commits into from
Sep 14, 2023
Merged

186 generalise rankcomparisongenerator class #192

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aeeccee
collapse separated methods in RankComparisonGenerator class to genera…
yaseminbridges Sep 12, 2023
4ec4d2b
tox lint
yaseminbridges Sep 12, 2023
405f742
specifying return types
yaseminbridges Sep 12, 2023
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59 changes: 23 additions & 36 deletions src/pheval/analyse/generate_summary_outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,29 +34,11 @@ def _calculate_rank_difference(self) -> pd.DataFrame:
comparison_df["rank_decrease"] = comparison_df.iloc[:, 3] - comparison_df.iloc[:, 2]
return comparison_df

def generate_gene_output(self, prefix: str) -> None:
"""Generate the output for gene prioritisation ranks."""
self._generate_dataframe().to_csv(prefix + "-gene_rank_comparison.tsv", sep="\t")
def generate_output(self, prefix: str, suffix: str) -> None:
self._generate_dataframe().to_csv(prefix + suffix, sep="\t")

def generate_variant_output(self, prefix: str) -> None:
"""Generate the output for variant prioritisation ranks."""
self._generate_dataframe().to_csv(prefix + "-variant_rank_comparison.tsv", sep="\t")

def generate_disease_output(self, prefix: str) -> None:
"""Generate the output for disease prioritisation ranks."""
self._generate_dataframe().to_csv(prefix + "-disease_rank_comparison.tsv", sep="\t")

def generate_gene_comparison_output(self, prefix: str) -> None:
"""Generate the output for gene prioritisation rank comparison."""
self._calculate_rank_difference().to_csv(prefix + "-gene_rank_comparison.tsv", sep="\t")

def generate_variant_comparison_output(self, prefix: str) -> None:
"""Generate the output for variant prioritisation rank comparison."""
self._calculate_rank_difference().to_csv(prefix + "-variant_rank_comparison.tsv", sep="\t")

def generate_disease_comparison_output(self, prefix: str) -> None:
"""Generate the output for disease prioritisation rank comparison."""
self._calculate_rank_difference().to_csv(prefix + "-disease_rank_comparison.tsv", sep="\t")
def generate_comparison_output(self, prefix: str, suffix: str) -> None:
self._calculate_rank_difference().to_csv(prefix + suffix, sep="\t")


class RankStatsWriter:
Expand Down Expand Up @@ -118,8 +100,8 @@ def generate_benchmark_gene_output(
prioritisation_data: TrackRunPrioritisation, plot_type: str
) -> None:
"""Generate gene prioritisation outputs for benchmarking single run."""
RankComparisonGenerator(prioritisation_data.gene_prioritisation.ranks).generate_gene_output(
f"{prioritisation_data.gene_prioritisation.results_dir.name}"
RankComparisonGenerator(prioritisation_data.gene_prioritisation.ranks).generate_output(
f"{prioritisation_data.gene_prioritisation.results_dir.name}", "-gene_rank_comparison.tsv"
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Technically this filename seems to violate SRP (because it exists more than once in the code).

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The construction of the full filename? Or the "-gene_rank_comparison.tsv" part?

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The string "-gene_rank_comparison.tsv" appears twice in that file.

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@yaseminbridges yaseminbridges Sep 12, 2023 •
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Ah yes! I plan on addressing this in #193. I have the code roughly written out with how I plan it to be structured and it avoids this (used a constant for _rank_comparison.tsv)

)
generate_plots(
[prioritisation_data],
Expand All @@ -134,9 +116,10 @@ def generate_benchmark_variant_output(
prioritisation_data: TrackRunPrioritisation, plot_type: str
) -> None:
"""Generate variant prioritisation outputs for benchmarking single run."""
RankComparisonGenerator(
prioritisation_data.variant_prioritisation.ranks
).generate_variant_output(f"{prioritisation_data.variant_prioritisation.results_dir.name}")
RankComparisonGenerator(prioritisation_data.variant_prioritisation.ranks).generate_output(
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@julesjacobsen I am sure this is one of the things where you believe Python has gone wrong over a beautiful Java OO design..

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Nope. The previous implementation was all useless repetition. No one wants that.

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I meant prioritisation_data.variant_prioritisation.ranks without encapsulation!

f"{prioritisation_data.variant_prioritisation.results_dir.name}",
"-variant_rank_comparison.tsv",
)
generate_plots(
[prioritisation_data],
TrackRunPrioritisation.return_variant,
Expand All @@ -150,9 +133,10 @@ def generate_benchmark_disease_output(
prioritisation_data: TrackRunPrioritisation, plot_type: str
) -> None:
"""Generate disease prioritisation outputs for benchmarking single run."""
RankComparisonGenerator(
prioritisation_data.disease_prioritisation.ranks
).generate_disease_output(f"{prioritisation_data.disease_prioritisation.results_dir.name}")
RankComparisonGenerator(prioritisation_data.disease_prioritisation.ranks).generate_output(
f"{prioritisation_data.disease_prioritisation.results_dir.name}",
"-disease_rank_comparison.tsv",
)
generate_plots(
[prioritisation_data],
TrackRunPrioritisation.return_disease,
Expand Down Expand Up @@ -184,11 +168,12 @@ def generate_gene_rank_comparisons(comparison_ranks: [tuple]) -> None:
merged_results = merge_results(
deepcopy(pair[0].gene_prioritisation.ranks), deepcopy(pair[1].gene_prioritisation.ranks)
)
RankComparisonGenerator(merged_results).generate_gene_comparison_output(
RankComparisonGenerator(merged_results).generate_comparison_output(
f"{pair[0].gene_prioritisation.results_dir.parents[0].name}_"
f"{pair[0].gene_prioritisation.results_dir.name}"
f"_vs_{pair[1].gene_prioritisation.results_dir.parents[0].name}_"
f"{pair[1].gene_prioritisation.results_dir.name}"
f"{pair[1].gene_prioritisation.results_dir.name}",
"-gene_rank_comparison.tsv",
)


Expand All @@ -199,11 +184,12 @@ def generate_variant_rank_comparisons(comparison_ranks: [tuple]) -> None:
deepcopy(pair[0].variant_prioritisation.ranks),
deepcopy(pair[1].variant_prioritisation.ranks),
)
RankComparisonGenerator(merged_results).generate_variant_comparison_output(
RankComparisonGenerator(merged_results).generate_comparison_output(
f"{pair[0].variant_prioritisation.results_dir.parents[0].name}_"
f"{pair[0].variant_prioritisation.results_dir.name}"
f"_vs_{pair[1].variant_prioritisation.results_dir.parents[0].name}_"
f"{pair[1].variant_prioritisation.results_dir.name}"
f"{pair[1].variant_prioritisation.results_dir.name}",
"-variant_rank_comparison.tsv",
)


Expand All @@ -214,11 +200,12 @@ def generate_disease_rank_comparisons(comparison_ranks: [tuple]) -> None:
deepcopy(pair[0].disease_prioritisation.ranks),
deepcopy(pair[1].disease_prioritisation.ranks),
)
RankComparisonGenerator(merged_results).generate_disease_comparison_output(
RankComparisonGenerator(merged_results).generate_comparison_output(
f"{pair[0].disease_prioritisation.results_dir.parents[0].name}_"
f"{pair[0].disease_prioritisation.results_dir.name}"
f"_vs_{pair[1].disease_prioritisation.results_dir.parents[0].name}_"
f"{pair[1].disease_prioritisation.results_dir.name}"
f"{pair[1].disease_prioritisation.results_dir.name}",
"-disease_rank_comparison.tsv",
)


Expand Down