-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Group arguments together in dataclasses
- add CalculationArgs dataclass with arguments related to how the dataset is calculated - add OutputArgs dataclass with arguments related to the output
- Loading branch information
1 parent
6982ee6
commit c7e76b5
Showing
6 changed files
with
458 additions
and
565 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,172 @@ | ||
| import argparse | ||
| from dataclasses import dataclass | ||
|
|
||
|
|
||
| @dataclass(frozen=True) | ||
| class CalculationArgs: | ||
| """ | ||
| Collection of arguments related to how to calculate the dataset. | ||
| chembl_version: Version of ChEMBL for output file names | ||
| calculate_rdkit: True if RDKit-based compound properties should be calculated | ||
| limit_to_literature: Include only literature sources if True | ||
| limited_flag: String version of limit_to_literature used in file names | ||
| min_nof_cpds_bf: Minimum number of compounds per target for the BF subset | ||
| min_nof_cpds_b: Minimum number of compounds per target for the B subset | ||
| """ | ||
|
|
||
| chembl_version: str | ||
| calculate_rdkit: bool | ||
| limit_to_literature: bool | ||
| limited_flag: str | ||
| min_nof_cpds_bf: int | ||
| min_nof_cpds_b: int | ||
|
|
||
|
|
||
| @dataclass(frozen=True) | ||
| class OutputArgs: | ||
| """ | ||
| Collection of arguments related to how to output the dataset. | ||
| output_path: Path to write output files to | ||
| delimiter: Delimiter in csv-output | ||
| write_to_csv: True if output should be written to csv | ||
| write_to_excel: True if output should be written to excel | ||
| write_full_dataset: True if the full dataset should be written to output | ||
| write_bf: True if subsets based on binding+functional data should be written to output | ||
| write_b: True if subsets based on binding data only should be written to output | ||
| """ | ||
|
|
||
| output_path: str | ||
| delimiter: str | ||
| write_to_csv: bool | ||
| write_to_excel: bool | ||
| write_full_dataset: bool | ||
| write_bf: bool | ||
| write_b: bool | ||
|
|
||
|
|
||
| def parse_args() -> argparse.Namespace: | ||
| """ | ||
| Get arguments with argparse. | ||
| :return: Populated argparse.Namespace | ||
| :rtype: argparse.Namespace | ||
| """ | ||
| parser = argparse.ArgumentParser( | ||
| description="Extract the compound-target pairs dataset from ChEMBL. \ | ||
| The full dataset plus filtering columns for binding vs. binding+functional data \ | ||
| will always be written to csv. \ | ||
| Additional outputs and output types can be chosen with the parameters below." | ||
| ) | ||
|
|
||
| parser.add_argument( | ||
| "--chembl", | ||
| "-v", | ||
| dest="chembl_version", | ||
| metavar="<version>", | ||
| type=str, | ||
| default=None, | ||
| help="ChEMBL version. \ | ||
| Latest version if None. \ | ||
| Required if a path to a SQLite database is provided, \ | ||
| i.e., if --sqlite is set. (default: None)", | ||
| ) | ||
| parser.add_argument( | ||
| "--sqlite", | ||
| "-s", | ||
| metavar="<path>", | ||
| type=str, | ||
| default=None, | ||
| help="Path to SQLite database. \ | ||
| ChEMBL is downloaded as an SQLite database \ | ||
| and handled by chembl_downloader if None. (default: None)", | ||
| ) | ||
| parser.add_argument( | ||
| "--output", | ||
| "-o", | ||
| dest="output_path", | ||
| metavar="<path>", | ||
| type=str, | ||
| required=True, | ||
| help="Path to write the output file(s) to. (required)", | ||
| ) | ||
| parser.add_argument( | ||
| "--delimiter", | ||
| "-d", | ||
| metavar="<delimiter>", | ||
| type=str, | ||
| default=";", | ||
| help="Delimiter in output csv-files. (default: ;)", | ||
| ) | ||
| parser.add_argument( | ||
| "--all_sources", | ||
| action="store_true", | ||
| help="If this is set, the dataset is calculated based on all sources in ChEMBL. \ | ||
| This includes data from BindingDB which may skew the results. \ | ||
| Default (not set): the dataset is calculated based on only literature data.", | ||
| ) | ||
| parser.add_argument( | ||
| "--rdkit", | ||
| dest="calculate_rdkit", | ||
| action="store_true", | ||
| help="Calculate RDKit-based compound properties.", | ||
| ) | ||
| parser.add_argument( | ||
| "--excel", | ||
| dest="write_to_excel", | ||
| action="store_true", | ||
| help="Write the results to excel. Note: this may fail if the output is too large.", | ||
| ) | ||
| parser.add_argument( | ||
| "--BF", | ||
| dest="write_bf", | ||
| action="store_true", | ||
| help="Write binding+functional data subsets.", | ||
| ) | ||
| parser.add_argument( | ||
| "--B", dest="write_b", action="store_true", help="Write binding data subsets." | ||
| ) | ||
| parser.add_argument( | ||
| "--debug", action="store_true", help="Log additional debugging information." | ||
| ) | ||
| args = parser.parse_args() | ||
|
|
||
| return args | ||
|
|
||
|
|
||
| def get_args() -> tuple[argparse.Namespace, CalculationArgs, OutputArgs]: | ||
| """ | ||
| Get parsed and default arguments. | ||
| :return: parserd arguments, | ||
| arguments related to how to calculate the dataset as CalculationArgs, | ||
| arguments related to how to output the dataset as OutputArgs | ||
| :rtype: tuple[argparse.Namespace, CalculationArgs, OutputArgs] | ||
| """ | ||
| args = parse_args() | ||
|
|
||
| calc_args = CalculationArgs( | ||
| chembl_version=args.chembl_version, | ||
| calculate_rdkit=args.calculate_rdkit, | ||
| limit_to_literature=not args.all_sources, | ||
| # used in file names | ||
| limited_flag="literature_only" if not args.all_sources else "all_sources", | ||
| min_nof_cpds_bf=100, | ||
| min_nof_cpds_b=100, | ||
| ) | ||
|
|
||
| output_args = OutputArgs( | ||
| output_path=args.output_path, | ||
| delimiter=args.delimiter, | ||
| # Always write the results to csv. | ||
| write_to_csv=True, | ||
| write_to_excel=args.write_to_excel, | ||
| # Always write the full dataset plus filtering columns | ||
| # for binding vs. binding+functional data. | ||
| write_full_dataset=True, | ||
| write_bf=args.write_bf, | ||
| write_b=args.write_b, | ||
| ) | ||
|
|
||
| return args, calc_args, output_args |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.