Sourcery refactored master branch #4
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| if reads2: | ||
| if output2 is None: | ||
| raise click.UsageError(f'If paired reads are specified, you must ' | ||
| f'specify an output file for the filtered ' | ||
| f'reverse reads with `-O/--output2`!') | ||
| if reads2 and output2 is None: | ||
| raise click.UsageError(f'If paired reads are specified, you must ' | ||
| f'specify an output file for the filtered ' | ||
| f'reverse reads with `-O/--output2`!') |
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Function main refactored with the following changes:
- Merge nested if conditions
- Remove redundant conditional
| if node is not None: | ||
| all_taxids = node.taxids_set() | ||
| else: | ||
| all_taxids = set() | ||
| all_taxids = node.taxids_set() if node is not None else set() |
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Function find_target_read_ids refactored with the following changes:
- Replace if statement with if expression
| if sciname == 'unclassified' or sciname == 'root': | ||
| if sciname in ['unclassified', 'root']: |
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Function TaxNode.build_taxonomy_tree refactored with the following changes:
- Replace multiple comparisons of same variable with
inoperator
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| if centrifuge_results is not None \ | ||
| and kraken2_results is not None \ | ||
| and tcr.kraken2_unclassified is not None \ | ||
| and tcr.kraken2_targets is not None \ | ||
| and tcr.centrifuge_unclassified is not None \ | ||
| and tcr.centrifuge_targets is not None: | ||
| n_target_uq_c = len(tcr.centrifuge_targets - tcr.kraken2_targets) | ||
| n_target_uq_k2 = len(tcr.kraken2_targets - tcr.centrifuge_targets) | ||
| n_target_total = len(target_read_ids) | ||
| logging.info(f'Total viral reads={n_target_total}') | ||
| logging.info(f'Centrifuge found n={n_target_uq_c} target reads not ' | ||
| f'found with Kraken2') | ||
| logging.info(f'Kraken2 found n={n_target_uq_k2} target reads not found' | ||
| f' with Centrifuge') | ||
| if ( | ||
| centrifuge_results is None | ||
| or kraken2_results is None | ||
| or tcr.kraken2_unclassified is None | ||
| or tcr.kraken2_targets is None | ||
| or tcr.centrifuge_unclassified is None | ||
| or tcr.centrifuge_targets is None | ||
| ): | ||
| return | ||
| n_target_uq_c = len(tcr.centrifuge_targets - tcr.kraken2_targets) | ||
| n_target_uq_k2 = len(tcr.kraken2_targets - tcr.centrifuge_targets) | ||
| n_target_total = len(target_read_ids) | ||
| logging.info(f'Total viral reads={n_target_total}') | ||
| logging.info(f'Centrifuge found n={n_target_uq_c} target reads not ' | ||
| f'found with Kraken2') | ||
| logging.info(f'Kraken2 found n={n_target_uq_k2} target reads not found' | ||
| f' with Centrifuge') | ||
|
|
||
| uc_uq_k2 = tcr.kraken2_unclassified - tcr.centrifuge_unclassified | ||
| uc_uq_c = tcr.centrifuge_unclassified - tcr.kraken2_unclassified | ||
| if tcr.centrifuge_df_results is not None \ | ||
| and isinstance(tcr.centrifuge_df_results, pd.DataFrame): | ||
| c_read_ids = set(tcr.centrifuge_df_results.index) | ||
| n_k2_not_in_centrifuge = len(uc_uq_k2 - c_read_ids) | ||
| if n_k2_not_in_centrifuge: | ||
| logging.info(f'N={n_k2_not_in_centrifuge} Unclassified reads ' | ||
| f'by Kraken2 not in Centrifuge results') | ||
| if tcr.kraken2_df_results is not None \ | ||
| and isinstance(tcr.kraken2_df_results, pd.DataFrame): | ||
| k2_read_ids = set(tcr.kraken2_df_results.index) | ||
| n_c_not_in_k2 = len(uc_uq_c - k2_read_ids) | ||
| if n_c_not_in_k2: | ||
| logging.info(f'N={n_c_not_in_k2} Unclassified reads by ' | ||
| f'Centrifuge not in Kraken2 results') | ||
| if tcr.centrifuge_unclassified and tcr.kraken2_unclassified: | ||
| uc_intersect = tcr.centrifuge_unclassified \ | ||
| & tcr.kraken2_unclassified | ||
| logging.info(f'N={len(uc_intersect)} reads unclassified by both ' | ||
| f'Centrifuge and Kraken2.') | ||
| uc_uq_k2 = tcr.kraken2_unclassified - tcr.centrifuge_unclassified | ||
| uc_uq_c = tcr.centrifuge_unclassified - tcr.kraken2_unclassified | ||
| if tcr.centrifuge_df_results is not None \ | ||
| and isinstance(tcr.centrifuge_df_results, pd.DataFrame): | ||
| c_read_ids = set(tcr.centrifuge_df_results.index) | ||
| n_k2_not_in_centrifuge = len(uc_uq_k2 - c_read_ids) | ||
| if n_k2_not_in_centrifuge: | ||
| logging.info(f'N={n_k2_not_in_centrifuge} Unclassified reads ' | ||
| f'by Kraken2 not in Centrifuge results') | ||
| if tcr.kraken2_df_results is not None \ | ||
| and isinstance(tcr.kraken2_df_results, pd.DataFrame): | ||
| k2_read_ids = set(tcr.kraken2_df_results.index) | ||
| n_c_not_in_k2 = len(uc_uq_c - k2_read_ids) | ||
| if n_c_not_in_k2: | ||
| logging.info(f'N={n_c_not_in_k2} Unclassified reads by ' | ||
| f'Centrifuge not in Kraken2 results') | ||
| if tcr.centrifuge_unclassified and tcr.kraken2_unclassified: | ||
| uc_intersect = tcr.centrifuge_unclassified \ | ||
| & tcr.kraken2_unclassified | ||
| logging.info(f'N={len(uc_intersect)} reads unclassified by both ' | ||
| f'Centrifuge and Kraken2.') |
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Function compare_kraken2_and_centrifuge refactored with the following changes:
- Add guard clause
| return sum([1 for l in f]) | ||
| return sum(1 for l in f) |
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Function count_lines refactored with the following changes:
- Replace unneeded comprehension with generator
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Branch
masterrefactored by Sourcery.If you're happy with these changes, merge this Pull Request using the Squash and merge strategy.
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