pythonflex 0.3.3__py3-none-any.whl → 0.4__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.
- pythonflex/__init__.py +28 -4
- pythonflex/analysis.py +287 -578
- pythonflex/examples/basic_usage.py +40 -32
- pythonflex/examples/manuscript.py +37 -42
- pythonflex/examples/runtime/runtime_benchmark.py +218 -0
- pythonflex/examples/runtime/runtime_benchmark_10_runs_memmap.py +534 -0
- pythonflex/examples/runtime/runtime_benchmark_corum_njobs.py +245 -0
- pythonflex/examples/runtime/runtime_benchmark_gobp_njobs_chunks.py +319 -0
- pythonflex/examples/runtime/runtime_benchmark_gobp_optimization.py +417 -0
- pythonflex/examples/runtime/runtime_benchmark_repeated.py +347 -0
- pythonflex/old_functions.py +422 -0
- pythonflex/plotting.py +655 -242
- pythonflex/preprocessing.py +62 -60
- pythonflex/utils.py +36 -9
- {pythonflex-0.3.3.dist-info → pythonflex-0.4.dist-info}/METADATA +9 -4
- pythonflex-0.4.dist-info/RECORD +32 -0
- {pythonflex-0.3.3.dist-info → pythonflex-0.4.dist-info}/WHEEL +1 -1
- pythonflex-0.4.dist-info/licenses/LICENSE +7 -0
- pythonflex-0.3.3.dist-info/RECORD +0 -24
- {pythonflex-0.3.3.dist-info → pythonflex-0.4.dist-info}/entry_points.txt +0 -0
pythonflex/__init__.py
CHANGED
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@@ -1,20 +1,44 @@
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from .logging_config import log
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from .utils import dsave, dload
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from .preprocessing import get_example_data_path, load_datasets, get_common_genes, filter_matrix_by_genes, load_gold_standard, filter_duplicate_terms
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from .analysis import initialize, pra, pra_percomplex, fast_corr, perform_corr, is_symmetric, binary, has_mirror_of_first_pair, convert_full_to_half_matrix, drop_mirror_pairs, quick_sort, complex_contributions, save_results_to_csv, update_matploblib_config, mpr_prepare
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from .analysis import initialize, prepare_terms_for_dataset, pra, pra_percomplex, fast_corr, perform_corr, is_symmetric, binary, has_mirror_of_first_pair, convert_full_to_half_matrix, drop_mirror_pairs, quick_sort, complex_contributions, save_results_to_csv, update_matploblib_config, mpr_prepare
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from .plotting import (
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adjust_text_positions, plot_precision_recall_curve, plot_aggregated_pra, plot_iqr_pra, plot_all_runs_pra, plot_percomplex_scatter,
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plot_percomplex_scatter_bysize, plot_complex_contributions, plot_significant_complexes, plot_auc_scores,
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plot_mpr_tp, plot_mpr_complexes, plot_mpr_tp_multi, plot_mpr_complexes_multi, plot_mpr_complexes_auc_scores
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plot_mpr_tp, plot_mpr_complexes, plot_mpr_tp_multi, plot_mpr_complexes_multi, plot_mpr_complexes_auc_scores,
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plot_mpr_true_positive_curve, plot_mpr_complex_coverage_curve, plot_mpr_complex_auc_scores, plot_mpr_summary
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)
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def main():
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import argparse
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from importlib.metadata import PackageNotFoundError, version
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try:
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package_version = version("pythonflex")
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except PackageNotFoundError:
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package_version = "unknown"
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parser = argparse.ArgumentParser(
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prog="pythonflex",
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description="pythonFLEX benchmarking toolkit. Use the Python API to run analyses.",
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)
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parser.add_argument(
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"--version",
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action="version",
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version=f"pythonflex {package_version}",
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)
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parser.parse_args()
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parser.print_help()
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__all__ = [ "log", "get_example_data_path", "fast_corr",
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"initialize", "dsave", "dload", "load_datasets", "get_common_genes",
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"filter_matrix_by_genes", "load_gold_standard", "filter_duplicate_terms", "pra", "pra_percomplex",
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"prepare_terms_for_dataset",
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"perform_corr", "is_symmetric", "binary", "has_mirror_of_first_pair", "convert_full_to_half_matrix",
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"drop_mirror_pairs", "quick_sort", "complex_contributions", "adjust_text_positions", "plot_precision_recall_curve",
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"plot_aggregated_pra", "plot_iqr_pra", "plot_all_runs_pra", "plot_percomplex_scatter", "plot_percomplex_scatter_bysize", "plot_complex_contributions",
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"plot_significant_complexes", "plot_auc_scores", "plot_mpr_complexes_auc_scores", "save_results_to_csv", "update_matploblib_config",
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"plot_significant_complexes", "plot_auc_scores", "plot_mpr_complexes_auc_scores", "plot_mpr_complex_auc_scores", "save_results_to_csv", "update_matploblib_config",
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"mpr_prepare", "plot_mpr_tp", "plot_mpr_complexes",
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"plot_mpr_tp_multi", "plot_mpr_complexes_multi"
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"plot_mpr_tp_multi", "plot_mpr_complexes_multi", "plot_mpr_true_positive_curve",
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"plot_mpr_complex_coverage_curve", "plot_mpr_summary", "main"
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]
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