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Merge branch 'main' into develop
# Conflicts: # src/biocatalyzer/bioreactor.py
2 parents 9296c41 + 1a5e8ce commit 93d4cf4

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‎.github/workflows/main.yml‎

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branches:
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- main
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- develop
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push:
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branches:
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- main
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jobs:
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test:
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matrix:
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os:
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- ubuntu-latest
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- windows-latest
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- macos-latest
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python-version:
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- 3.8
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‎README.md‎

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biocatalyzer_cli <PATH_TO_COMPOUNDS> <OUTPUT_DIRECTORY> [--neutralize=<BOOL>] [--reaction_rules=<FILE_PATH>] [--organisms=<FILE_PATH>] [--patterns_to_remove=<FILE_PATH>] [--molecules_to_remove=<FILE_PATH>] [--min_atom_count=<INT>] [--match_ms_data=<BOOL>] [--ms_data_path=<FILE_PATH>] [--tolerance=<FLOAT>] [--n_jobs=<INT>]
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```
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| Argument | Example | Description | Default |
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|--------------------------------------|---------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| compounds <PATH_TO_COMPOUNDS> | `file.tsv` or `"smile1;smiles2;smile3;etc"` | The path to the file containing the compounds to use as reactants. Or ;-separated SMILES strings.<sup>1</sup> | |
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| output_directory <OUTPUT_DIRECTORY> | `output/directory/` | The path directory to save the results to. | |
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| neutralize | `True` or `False` | Whether to neutralize the compounds before predicting the products. In this case the new products will also be neutralized. | `False` |
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| reaction_rules | `file.tsv` or `None` | The path to the file containing the reaction rules to use.<sup>2</sup> | [all_reaction_rules_forward_no_smarts_duplicates_sample.tsv](src/biocatalyzer/data/reactionrules/all_reaction_rules_forward_no_smarts_duplicates_sample.tsv) |
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| organisms | `file.tsv` or `"org_id1;org_id2;org_id3;etc"` or `None` | The path to the file containing the organisms to use. Or ;-separated organisms identifiers. Reaction Rules will be selected accordingly (select only rules associated with enzymes encoded by genes from this organisms).<sup>3</sup> | All reaction rules are used. |
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| patterns_to_remove | `patterns.tsv` or `None` | The path to the file containing the patterns to remove from the products. <sup>4</sup> | [patterns.tsv](src/biocatalyzer/data/patterns_to_remove/patterns.tsv) |
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| molecules_to_remove | `molecules.tsv` or `None` | The path to the file containing the molecules to remove from the products. <sup>5</sup> | [byproducts.tsv](src/biocatalyzer/data/byproducts_to_remove/byproducts.tsv) |
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| min_atom_count | `4` | The minimum number of heavy atoms a product must have. | `5` |
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| match_ms_data | `True` or `False` | Whether to match the predicted products to the MS data. | `False` |
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| ms_data_path | `ms_data.tsv` | The path to the file containing the MS data. <sup>6</sup> | `None` |
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| tolerance | `0.02` | The mass tolerance to use when matching masses. | `0.02` |
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| n_jobs | `6` | The number of jobs to run in parallel (-1 uses all). | `1` |
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| Argument | Example | Description | Default |
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|--------------------------------------|---------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| compounds <PATH_TO_COMPOUNDS> | `file.tsv` or `"smile1;smiles2;smile3;etc"` | The path to the file containing the compounds to use as reactants. Or ;-separated SMILES strings.<sup>1</sup> | |
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| output_directory <OUTPUT_DIRECTORY> | `output/directory/` | The path directory to save the results to. | |
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| neutralize | `True` or `False` | Whether to neutralize the compounds before predicting the products. In this case the new products will also be neutralized. | `False` |
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| reaction_rules | `file.tsv` or `None` | The path to the file containing the reaction rules to use.<sup>2</sup> | [all_reaction_rules_forward_no_smarts_duplicates_sample.tsv](src/biocatalyzer/data/reactionrules/all_reaction_rules_forward_no_smarts_duplicates_sample.tsv) |
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| organisms | `file.tsv` or `"org_id1;org_id2;org_id3;etc"` or `None` | The path to the file containing the organisms to use. Or ;-separated organisms identifiers. Reaction Rules will be selected accordingly (select only rules associated with enzymes encoded by genes from these organisms).<sup>3</sup> | All reaction rules are used. |
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| patterns_to_remove | `patterns.tsv` or `None` | The path to the file containing the patterns to remove from the products. <sup>4</sup> | [patterns.tsv](src/biocatalyzer/data/patterns_to_remove/patterns.tsv) |
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| molecules_to_remove | `molecules.tsv` or `None` | The path to the file containing the molecules to remove from the products. <sup>5</sup> | [byproducts.tsv](src/biocatalyzer/data/byproducts_to_remove/byproducts.tsv) |
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| min_atom_count | `4` | The minimum number of heavy atoms a product must have. | `5` |
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| match_ms_data | `True` or `False` | Whether to match the predicted products to the MS data. | `False` |
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| ms_data_path | `ms_data.tsv` | The path to the file containing the MS data. <sup>6</sup> | `None` |
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| tolerance | `0.02` | The mass tolerance to use when matching masses. | `0.02` |
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| n_jobs | `6` | The number of jobs to run in parallel (-1 uses all). | `1` |
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### Compounds
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‎src/biocatalyzer/bioreactor.py‎

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Tuple[pd.DataFrame, str]
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The processed results and the path to the results file.
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"""
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results = pd.read_csv(self._new_compounds_path, sep='\t', header=0)
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results = pd.read_csv(self._new_compounds_path, sep='\t', header=0, lineterminator='\n')
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results.EC_Numbers = results.EC_Numbers.fillna('')
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results = results.groupby(['OriginalCompoundID', 'NewCompoundSmiles']).agg({'OriginalCompoundSmiles': 'first',
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'OriginalReactionRuleID': ';'.join,

‎src/biocatalyzer/clis/cli.py‎

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output_path: Path to the output directory.
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"""
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logging.basicConfig(filename=f'{output_path}logging.log', level=logging.DEBUG)
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if reaction_rules is None:
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logging.info(f"Using default reaction rules file.")
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reaction_rules = os.path.join(
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DATA_FILES, '../data/reactionrules/reaction_rules_biocatalyzer.tsv.bz2')
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br = BioReactor(compounds_path=compounds,
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molecules_to_remove_path=molecules_to_remove,
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min_atom_count=min_atom_count,
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n_jobs=n_jobs)
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logging.basicConfig(filename=f'{output_path}logging.log', level=logging.DEBUG)
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br.react()
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_, new_results_path = br.process_results()
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raise ValueError("The path to the MS data file is required when matching MS data.")
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else:
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logging.info(f"Matching MS data.")
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ms = MSDataMatcher(ms_data_path=ms_data_path,
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compounds_to_match_path=new_results_path,
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output_path=output_path,

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