feat: Add wrapper for Tandem Repeat Finder (TRF) utility #4160
Conversation
…tputs as seen on the official repository.
…e and logic, unit test sample, stdout stderr to log file directive
📝 WalkthroughWalkthroughThis change introduces a new Snakemake wrapper for the Tandem Repeat Finder (TRF) tool, including environment specifications, metadata, wrapper implementation, test workflows, sample data, and automated test cases. The additions enable reproducible TRF runs within Snakemake, with parameter validation, logging, and comprehensive testing of wrapper behavior. Changes
Sequence Diagram(s)sequenceDiagram
participant Snakemake
participant Wrapper (wrapper.py)
participant TRF Tool
Snakemake->>Wrapper (wrapper.py): Provide input, output, params, log
Wrapper (wrapper.py)->>Wrapper (wrapper.py): Validate/parse params and flags
Wrapper (wrapper.py)->>Wrapper (wrapper.py): Prepare command and output directory
Wrapper (wrapper.py)->>TRF Tool: Execute TRF with constructed command
TRF Tool-->>Wrapper (wrapper.py): Generate output files
Wrapper (wrapper.py)-->>Snakemake: Completion and log handling
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Actionable comments posted: 5
🧹 Nitpick comments (12)
bio/trf/utils/__init__.py (1)
1-4: Add a final newline to satisfy Pylint convention
Static analysis flagged a missing final newline (C0304). Please ensure the file ends with a newline to adhere to style guidelines.🧰 Tools
🪛 Pylint (3.3.7)
[convention] 4-4: Final newline missing
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bio/trf/environment.yaml (1)
1-8: Standardize version specifiers in environment YAML
In Conda environment files, version pins are typically written without spaces around the equals sign (e.g.,trf=4.09rather thantrf =4.09). Consider updating both entries for consistency and clarity.bio/trf/test/Snakefile (1)
9-16: Potential output directory conflicts between rules.All three rules use the same output directory pattern
"trf_output/{sample}", which could cause conflicts if multiple rules target the same sample or if rules are run in parallel. Consider using rule-specific prefixes.rule run_trf_basic_with_defaults_nolog: input: sample="demo_data/{sample}.fasta", output: - directory("trf_output/{sample}"), + directory("trf_output/basic_defaults/{sample}"), wrapper: "master/bio/trf"bio/trf/utils/logger_utils/logger_config.py (1)
16-21: Consider improving type annotation for log_file_path parameter.The
log_file_pathparameter should be optional since file logging can be disabled, but it's currently typed as requiredstr.def setup_logger( name: str, - log_file_path: str, + log_file_path: str | None, log_level: int = logging.INFO, enable_file: bool = True, ) -> logging.Logger:bio/trf/utils/filteration/split_params_utils.py (1)
37-137: Consider refactoring this function to reduce complexity.The
split_trf_paramsfunction has high cyclomatic complexity with 20 local variables, 23 branches, and 62 statements. While the logic is correct, breaking it down into smaller helper functions would improve maintainability and testability.Consider extracting these logical sections into separate helper functions:
- Parameter validation and normalization (lines 57-69)
- Malformed option detection (lines 78-83)
- Non-flag token handling (lines 84-93)
- Flag with value parsing (lines 95-109)
- Option with value parsing (lines 111-121)
- Flag processing (lines 123-135)
Example refactoring approach:
+def _process_numeric_params(params_lower, logger): + """Extract and validate numeric parameters.""" + trf_numeric_params = {} + for key, value in params_lower.items(): + if key in TRF_NUMERIC_KEYS: + trf_numeric_params[key] = value + elif key != "extra": + logger.warning(TRF_MESSAGES["UNKNOWN_NUMERIC_PARAM"](key, value)) + return trf_numeric_params + +def _process_token(token, i, tokens, trf_flags, trf_options_with_values, logger): + """Process a single token and return the new index.""" + # Token processing logic here + # Return (new_index, updated_flags, updated_options) + pass🧰 Tools
🪛 Pylint (3.3.7)
[refactor] 37-37: Too many local variables (20/15)
(R0914)
[refactor] 37-37: Too many branches (23/12)
(R0912)
[refactor] 37-37: Too many statements (62/50)
(R0915)
bio/trf/test/tests.smk (1)
62-62: Fix typo in rule name.The rule name has a double underscore that appears to be unintentional.
-rule run_trf_permissible__optional_flag_with_mistake: +rule run_trf_permissible_optional_flag_with_mistake:bio/trf/utils/filteration/constants.py (1)
15-15: Fix typo in comment.-in other TRF parameter parsing utiliti(y/es). +in other TRF parameter parsing utilities.bio/trf/wrapper.py (3)
1-8: Fix typo in module docstring.There's a typo in the docstring: "recommened" should be "recommended".
- to recommened parameter values and flags for an ease of + to recommended parameter values and flags for an ease of
21-21: Consider making log file path configurable.The hardcoded log file path "logs/trf_run_by_logger.log" might cause issues in different execution contexts or when multiple instances run concurrently.
Consider making this path relative to the output directory or allowing configuration:
-logger = setup_logger("trf_logger", "logs/trf_run_by_logger.log", logging.INFO) +log_dir = Path(snakemake.output[0]).resolve() / "logs" +logger = setup_logger("trf_logger", str(log_dir / "trf_run_by_logger.log"), logging.INFO)
63-63: Document the exit code 3 handling.The shell command allows exit code 3 to be ignored. This should be documented to explain why this specific exit code is acceptable.
Add a comment explaining why exit code 3 is allowed:
+# TRF returns exit code 3 in some normal completion scenarios shell(f"( {cmd} || [ $? -eq 3 ] ) {log_redirect}")bio/trf/meta.yaml (1)
26-26: Fix YAML formatting issues.The file has several formatting issues that should be corrected for proper YAML standards:
- Trailing spaces on multiple lines
- Missing newline at end of file
- Flags are default to `-m -f -d`, in case the user doesn't specify a flag. Flag(s) are specified using the 'extra' param (e.g., '-d -h'). + Flags are default to `-m -f -d`, in case the user doesn't specify a flag. Flag(s) are specified using the 'extra' param (e.g., '-d -h').- If you choose `logs` directory to log in, kindly don't use this file name: **trf_run_by_logger.log**. This is reserved for logger input information. + If you choose `logs` directory to log in, kindly don't use this file name: **trf_run_by_logger.log**. This is reserved for logger input information.- The wrapper has been made as flexible as possible but there is room for adding more flexibility like supporting advance typing catches `-l = 20` etc., but this has been not catered + The wrapper has been made as flexible as possible but there is room for adding more flexibility like supporting advance typing catches `-l = 20` etc., but this has been not catered- Note: As this is a wrapper for TRF utility, it comes with it's limitations or defects if any. + Note: As this is a wrapper for TRF utility, it comes with it's limitations or defects if any. +Also applies to: 32-32, 42-42, 46-46
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🪛 YAMLlint (1.37.1)
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test_wrappers.py (1)
6980-6988: Consider breaking up long lines for better readability.While the current format is functional, the very long file path comparisons in the
compare_results_with_expecteddictionary could be formatted with line breaks for better maintainability:compare_results_with_expected={ - "trf_output/small_test/small_test.fasta.2.7.7.80.10.50.500.dat": "expected/small_test.fasta.2.7.7.80.10.50.500.dat", + "trf_output/small_test/small_test.fasta.2.7.7.80.10.50.500.dat": ( + "expected/small_test.fasta.2.7.7.80.10.50.500.dat" + ),🧰 Tools
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📜 Review details
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bio/trf/test/expected/small_test.fasta.2.7.7.80.10.50.500.datis excluded by!**/*.dat
📒 Files selected for processing (30)
bio/trf/config/__init__.py(1 hunks)bio/trf/config/constants.py(1 hunks)bio/trf/config/trf_config.py(1 hunks)bio/trf/environment.linux-64.pin.txt(1 hunks)bio/trf/environment.yaml(1 hunks)bio/trf/meta.yaml(1 hunks)bio/trf/test/Snakefile(1 hunks)bio/trf/test/demo_data/small_test.fasta(1 hunks)bio/trf/test/expected/small_test.fasta.2.7.7.80.10.50.500.mask(1 hunks)bio/trf/test/expected/small_test.fasta.2.7.7.80.10.50.500.summary.html(1 hunks)bio/trf/test/expected/small_test.fasta.s1.2.7.7.80.10.50.500.1.html(1 hunks)bio/trf/test/expected/small_test.fasta.s1.2.7.7.80.10.50.500.1.txt.html(1 hunks)bio/trf/test/expected/small_test.fasta.s2.2.7.7.80.10.50.500.1.html(1 hunks)bio/trf/test/expected/small_test.fasta.s2.2.7.7.80.10.50.500.1.txt.html(1 hunks)bio/trf/test/expected/small_test.fasta.s3.2.7.7.80.10.50.500.1.html(1 hunks)bio/trf/test/expected/small_test.fasta.s3.2.7.7.80.10.50.500.1.txt.html(1 hunks)bio/trf/test/tests.smk(1 hunks)bio/trf/utils/__init__.py(1 hunks)bio/trf/utils/filteration/__init__.py(1 hunks)bio/trf/utils/filteration/constants.py(1 hunks)bio/trf/utils/filteration/split_params_utils.py(1 hunks)bio/trf/utils/logger_utils/__init__.py(1 hunks)bio/trf/utils/logger_utils/constants.py(1 hunks)bio/trf/utils/logger_utils/log_utils.py(1 hunks)bio/trf/utils/logger_utils/logger_config.py(1 hunks)bio/trf/utils/validation/__init__.py(1 hunks)bio/trf/utils/validation/constants.py(1 hunks)bio/trf/utils/validation/validation_utils.py(1 hunks)bio/trf/wrapper.py(1 hunks)test_wrappers.py(5 hunks)
🧰 Additional context used
📓 Path-based instructions (2)
`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
bio/trf/utils/__init__.pybio/trf/utils/logger_utils/constants.pybio/trf/utils/validation/__init__.pybio/trf/config/constants.pybio/trf/utils/logger_utils/log_utils.pybio/trf/utils/validation/constants.pybio/trf/utils/filteration/__init__.pybio/trf/utils/filteration/constants.pybio/trf/utils/logger_utils/logger_config.pybio/trf/utils/logger_utils/__init__.pybio/trf/wrapper.pytest_wrappers.pybio/trf/config/__init__.pybio/trf/utils/filteration/split_params_utils.pybio/trf/utils/validation/validation_utils.pybio/trf/config/trf_config.py
`**/wrapper.py`: Do not complain about use of undefined variable called `snakemake`.
**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.
bio/trf/wrapper.py
🧬 Code Graph Analysis (3)
bio/trf/utils/validation/__init__.py (1)
bio/trf/utils/validation/validation_utils.py (2)
validate_trf_numeric_params(24-69)validate_trf_option_values(72-113)
bio/trf/utils/logger_utils/__init__.py (2)
bio/trf/utils/logger_utils/log_utils.py (1)
log_output_dir_contents(12-42)bio/trf/utils/logger_utils/logger_config.py (1)
setup_logger(16-88)
bio/trf/wrapper.py (5)
bio/trf/config/trf_config.py (5)
TRFConfig(29-139)update_params(62-76)update_flags_bool(78-94)update_flags_with_value(96-112)build_command(114-139)bio/trf/utils/filteration/split_params_utils.py (1)
split_trf_params(37-137)bio/trf/utils/logger_utils/log_utils.py (1)
log_output_dir_contents(12-42)bio/trf/utils/logger_utils/logger_config.py (1)
setup_logger(16-88)bio/trf/utils/validation/validation_utils.py (2)
validate_trf_numeric_params(24-69)validate_trf_option_values(72-113)
🪛 Pylint (3.3.7)
bio/trf/utils/__init__.py
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bio/trf/wrapper.py
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test_wrappers.py
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bio/trf/utils/filteration/split_params_utils.py
[refactor] 37-37: Too many local variables (20/15)
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[refactor] 37-37: Too many branches (23/12)
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[refactor] 37-37: Too many statements (62/50)
(R0915)
bio/trf/utils/validation/validation_utils.py
[warning] 51-51: Consider explicitly re-raising using 'except ValueError as exc' and 'raise ValueError(f"TRF parameter '{key}' must be an integer, got: {value}.") from exc'
(W0707)
[warning] 99-99: Consider explicitly re-raising using 'except ValueError as exc' and 'raise ValueError(f'Value for {flag} must be an integer, got: {value}') from exc'
(W0707)
🪛 YAMLlint (1.37.1)
bio/trf/meta.yaml
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🪛 Ruff (0.11.9)
bio/trf/wrapper.py
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bio/trf/utils/validation/validation_utils.py
51-51: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling
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99-99: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling
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- GitHub Check: Summary
🔇 Additional comments (41)
bio/trf/environment.linux-64.pin.txt (1)
1-31: Auto-generated conda pin file: no review required.
This file is generated by Conda to lock exact package builds and hashes for reproducibility.bio/trf/test/expected/small_test.fasta.2.7.7.80.10.50.500.mask (1)
1-31: Non-code file (FASTA output): no review needed.
This is an expected-mask FASTA used for test verification.bio/trf/test/demo_data/small_test.fasta (1)
1-24: Non-code file (FASTA input): no review needed.
This is test input data for the TRF wrapper.bio/trf/test/expected/small_test.fasta.2.7.7.80.10.50.500.summary.html (1)
1-29: Skip review for static test artifact.
This HTML summary is a golden output used for validating the TRF Snakemake wrapper and contains no executable logic.bio/trf/test/expected/small_test.fasta.s1.2.7.7.80.10.50.500.1.txt.html (1)
1-68: Skip review for static test artifact.
This HTML report is part of the expected outputs for TRF wrapper tests and doesn’t require code-level review.bio/trf/test/expected/small_test.fasta.s3.2.7.7.80.10.50.500.1.txt.html (1)
1-188: Skip review for static test artifact.
A large pre-generated HTML output serving as a golden file for test validation; no logic changes to assess.bio/trf/test/expected/small_test.fasta.s3.2.7.7.80.10.50.500.1.html (1)
1-28: Skip review for static HTML output.
This is a static test artifact generated by TRF and not subject to code review.bio/trf/utils/logger_utils/__init__.py (1)
16-19: Re-exported logging utilities are consistent.
The imported symbols (DEBUG_FORMATTER,FILE_HANDLER,NORMAL_FORMATTER,log_output_dir_contents,setup_logger) match the entries in__all__, providing a clear public API for logging configuration.bio/trf/test/expected/small_test.fasta.s1.2.7.7.80.10.50.500.1.html (1)
1-28: LGTM! Well-structured TRF output test file.This HTML file correctly represents the expected output format from TRF version 4.09. The structure includes proper citation information, sequence parameters, and a well-formatted results table. This test artifact will help ensure the TRF wrapper produces consistent and correct output.
bio/trf/test/expected/small_test.fasta.s2.2.7.7.80.10.50.500.1.html (1)
1-28: LGTM! Comprehensive test coverage with multiple sequences.This HTML file provides test coverage for a second sequence (length 84) with different tandem repeat analysis results. The consistent TRF output format across multiple test files ensures robust validation of the wrapper functionality.
bio/trf/utils/logger_utils/log_utils.py (1)
12-42: Excellent implementation with robust error handling.The
log_output_dir_contentsfunction is well-designed with several strong points:
- Proper use of keyword-only arguments for the logger parameter
- Robust error handling for non-existent directories
- Cross-platform compatibility using
Pathobjects- Informative logging messages including file counts and sizes
- Appropriate logging levels (warning for errors, info for normal operation)
The implementation follows Python best practices and provides valuable debugging information for TRF wrapper execution.
bio/trf/utils/logger_utils/constants.py (1)
8-21: Well-designed logging configuration constants.The logging constants provide excellent configurability:
DEBUG_FORMATTERincludes comprehensive information (level, timestamp, logger name) ideal for development and debuggingNORMAL_FORMATTERoffers a clean, production-friendly formatFILE_HANDLERuses sensible defaults: 5MB file size limit prevents excessive disk usage, 3 backup files provide good history retention, and UTF-8 encoding ensures proper character handlingThis centralized configuration approach promotes consistency across the TRF wrapper's logging system.
bio/trf/test/expected/small_test.fasta.s2.2.7.7.80.10.50.500.1.txt.html (1)
1-77: Skip review for static expected output artifact.This file serves as a static HTML fixture for integration tests and contains no executable code to review.
bio/trf/utils/validation/__init__.py (1)
1-23: Module exports for validation utilities look correct.The imports from
constantsandvalidation_utilsmatch what’s exposed in__all__, and the docstring accurately describes the public API.bio/trf/config/constants.py (1)
1-37: Default TRF configuration constants correctly defined.The
TRF_DEFAULT_PARAMS,TRF_DEFAULT_FLAGS_WITH_VALUE, andTRF_DEFAULT_FLAGS_BOOLdictionaries align with the TRF author’s recommended defaults (as referenced in the docstring), providing a clear and maintainable base configuration.bio/trf/utils/validation/constants.py (1)
1-48: Validation constraint dictionaries appear comprehensive and consistent.
TRF_NUMERIC_CONSTRAINTSandTRF_OPTION_VALUE_CONSTRAINTScover all required parameters and flags with appropriate bounds, allowed sets, and warning thresholds. The docstring clearly documents their purpose and structure.bio/trf/utils/filteration/__init__.py (1)
1-34: Public interface for parameter splitting correctly defined.The module cleanly re-exports
split_trf_paramsalong with its associated constants (TRF_NUMERIC_KEYS,TRF_VALID_FLAGS,TRF_VALID_OPTIONS_WITH_VALUES,TRF_MESSAGES) as specified in the docstring and__all__. This aligns well with the wrapper’s parameter parsing requirements.bio/trf/test/Snakefile (2)
20-37: Good example demonstrating full parameter specification.This rule effectively demonstrates how to use all available TRF parameters with explicit logging configuration.
43-55: Effective demonstration of partial parameter override.This rule clearly shows how the wrapper handles partial parameter specification while maintaining defaults for unspecified parameters.
bio/trf/utils/logger_utils/logger_config.py (1)
68-71: Good defensive programming for directory creation.The logic properly checks for directory existence and creates it if needed using
exist_ok=Trueto handle race conditions.bio/trf/config/__init__.py (1)
1-31: Well-structured module interface with clear documentation.The module provides a clean public API with proper
__all__definition and comprehensive docstring explaining the exposed components.bio/trf/config/trf_config.py (3)
56-60: Good use of dataclass with proper default factories.The implementation correctly uses
default_factoryto avoid mutable default arguments and properly deep copies the default parameters.
131-139: Command building logic is well-structured.The method effectively combines all parameter types into a coherent command string with proper formatting and spacing.
127-129:⚠️ Potential issueLogic issue: Always overrides user flags with defaults.
The current condition
if not self.flags_with_value and not self.flags_bool:uses AND logic, meaning defaults are only applied when BOTH dictionaries are empty. However, if a user provides only boolean flags or only value flags, the other type gets set to defaults, potentially overriding user intent.Consider this scenario: user provides
flags_bool = {"h": True}but noflags_with_value. The current logic will overrideflags_with_valuewith defaults, which may not be intended.- if not self.flags_with_value and not self.flags_bool: + # Only set defaults if no flags have been configured at all + if not self.flags_with_value and not self.flags_bool: self.flags_with_value = copy.deepcopy(TRF_DEFAULT_FLAGS_WITH_VALUE) self.flags_bool = copy.deepcopy(TRF_DEFAULT_FLAGS_BOOL) + elif not self.flags_with_value: + # User provided bool flags but no value flags - use empty dict for value flags + pass + elif not self.flags_bool: + # User provided value flags but no bool flags - use empty dict for bool flags + passLikely an incorrect or invalid review comment.
bio/trf/utils/filteration/split_params_utils.py (1)
57-137: Well-implemented parameter parsing logic!The function correctly handles multiple input formats, case-insensitive matching, and provides clear error messages for malformed inputs. The logging approach is appropriate for warning about ignored parameters while raising exceptions for critical errors.
bio/trf/test/tests.smk (1)
1-113: Excellent test coverage!The test suite comprehensively covers various scenarios including:
- Invalid file type handling
- Invalid parameter values
- Different flag input styles
- Error cases with malformed flags
- Missing log directive behavior
This provides robust validation of the TRF wrapper's error handling and parameter parsing capabilities.
bio/trf/utils/filteration/constants.py (1)
20-56: Well-structured constants and message templates!The module provides a clean separation of concerns with:
- Efficient set-based lookups for parameter validation
- Comprehensive regex patterns for input parsing
- Consistent error message formatting using lambda templates
This design promotes maintainability and makes it easy to extend with new parameters or flags.
bio/trf/wrapper.py (2)
46-46: Document the necessity of changing working directory.The
os.chdir()call changes the global working directory, which can have side effects. Please ensure this is necessary for TRF execution and consider if there are alternative approaches.Is changing the working directory necessary for TRF to function correctly? Consider if the command can be executed with explicit paths instead.
48-67: Well-structured parameter processing and execution flow.The parameter processing, validation, and command execution flow is well-organized and follows good practices:
- Proper separation of concerns with dedicated validation functions
- Configuration object pattern for managing parameters
- Comprehensive logging of the process
🧰 Tools
🪛 Ruff (0.11.9)
50-50: Undefined name
snakemake(F821)
🪛 Pylint (3.3.7)
[error] 50-50: Undefined variable 'snakemake'
(E0602)
bio/trf/meta.yaml (1)
1-46: Comprehensive and well-structured metadata.The metadata file provides excellent documentation of the TRF wrapper interface, including:
- Clear parameter descriptions with defaults and constraints
- Detailed usage notes and examples
- Appropriate warnings about limitations and reserved file names
- Good integration guidance for developers
🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 26-26: trailing spaces
(trailing-spaces)
[error] 32-32: trailing spaces
(trailing-spaces)
[error] 42-42: trailing spaces
(trailing-spaces)
[error] 46-46: no new line character at the end of file
(new-line-at-end-of-file)
[error] 46-46: trailing spaces
(trailing-spaces)
bio/trf/utils/validation/validation_utils.py (1)
24-70: Well-designed validation functions with comprehensive constraint checking.Both validation functions demonstrate excellent design:
- Clear separation of concerns between numeric parameters and option values
- Comprehensive constraint validation (min, max, allowed values, recommendations)
- Proper logging integration for warnings about unknown parameters
- Good error messages that help users understand validation failures
- Graceful handling of unknown parameters with warnings rather than errors
Also applies to: 72-113
🧰 Tools
🪛 Ruff (0.11.9)
51-51: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
🪛 Pylint (3.3.7)
[warning] 51-51: Consider explicitly re-raising using 'except ValueError as exc' and 'raise ValueError(f"TRF parameter '{key}' must be an integer, got: {value}.") from exc'
(W0707)
test_wrappers.py (10)
158-158: LGTM! Good formatting improvement.The empty line addition improves code readability and follows Python formatting conventions.
1268-1281: LGTM! Good formatting improvements.The addition of trailing commas in the function call arguments improves consistency and makes future diffs cleaner when adding new arguments.
2067-2069: LGTM! Improved code formatting and readability.The proper line breaks and indentation for the commented code and dictionary formatting enhance readability.
🧰 Tools
🪛 Pylint (3.3.7)
[convention] 2067-2067: Line too long (162/100)
(C0301)
2114-2119: LGTM! Good formatting consistency.The trailing comma addition and proper line formatting maintain consistency with the rest of the codebase.
🧰 Tools
🪛 Pylint (3.3.7)
[convention] 2118-2118: Line too long (130/100)
(C0301)
6962-6991: Excellent comprehensive test for TRF basic functionality.The test properly validates the basic TRF wrapper functionality with default parameters and includes comprehensive output file validation using
compare_results_with_expected. The test covers all expected output file types (.dat, .mask, .html, .txt.html) which ensures the wrapper generates complete results.🧰 Tools
🪛 Pylint (3.3.7)
[convention] 6980-6980: Line too long (128/100)
(C0301)
[convention] 6981-6981: Line too long (130/100)
(C0301)
[convention] 6982-6982: Line too long (146/100)
(C0301)
[convention] 6983-6983: Line too long (140/100)
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[convention] 6984-6984: Line too long (148/100)
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[convention] 6985-6985: Line too long (140/100)
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[convention] 6986-6986: Line too long (148/100)
(C0301)
[convention] 6987-6987: Line too long (140/100)
(C0301)
[convention] 6988-6988: Line too long (148/100)
(C0301)
[convention] 6967-6967: Missing function or method docstring
(C0116)
[warning] 6967-6967: Redefining name 'run' from outer scope (line 41)
(W0621)
6993-7006: Good coverage of custom parameter functionality.This test ensures the wrapper correctly handles all custom parameters, which is essential for the flexibility mentioned in the PR objectives.
🧰 Tools
🪛 Pylint (3.3.7)
[convention] 6993-6993: Missing function or method docstring
(C0116)
[warning] 6993-6993: Redefining name 'run' from outer scope (line 41)
(W0621)
7008-7021: Well-designed test for partial parameter handling.This test validates the feature mentioned in the PR objectives where partial parameters are combined with recommended defaults, ensuring robust parameter management.
🧰 Tools
🪛 Pylint (3.3.7)
[convention] 7008-7008: Missing function or method docstring
(C0116)
[warning] 7008-7008: Redefining name 'run' from outer scope (line 41)
(W0621)
7024-7054: Excellent error handling validation.These tests properly validate that the wrapper correctly handles invalid input files and parameter values by expecting
subprocess.CalledProcessError. This aligns with the PR objective of validating parameter values and flagging errors for disallowed options.🧰 Tools
🪛 Pylint (3.3.7)
[convention] 7024-7024: Missing function or method docstring
(C0116)
[warning] 7024-7024: Redefining name 'run' from outer scope (line 41)
(W0621)
[convention] 7040-7040: Missing function or method docstring
(C0116)
[warning] 7040-7040: Redefining name 'run' from outer scope (line 41)
(W0621)
7056-7119: Comprehensive flag validation testing.These tests thoroughly cover the flag validation functionality mentioned in the PR objectives, including:
- Permissible flags working correctly
- Error detection for flag mistakes
- Handling of additional features
- Processing of impermissible flags
This ensures robust parameter validation as specified in the requirements.
🧰 Tools
🪛 Pylint (3.3.7)
[convention] 7069-7069: Line too long (128/100)
(C0301)
[convention] 7056-7056: Missing function or method docstring
(C0116)
[warning] 7056-7056: Redefining name 'run' from outer scope (line 41)
(W0621)
[convention] 7074-7074: Missing function or method docstring
(C0116)
[warning] 7074-7074: Redefining name 'run' from outer scope (line 41)
(W0621)
[convention] 7090-7090: Missing function or method docstring
(C0116)
[warning] 7090-7090: Redefining name 'run' from outer scope (line 41)
(W0621)
[convention] 7106-7106: Missing function or method docstring
(C0116)
[warning] 7106-7106: Redefining name 'run' from outer scope (line 41)
(W0621)
7136-7149: Good logging directive validation.This test ensures the custom logging functionality works correctly, which supports the configurable logging modes mentioned in the PR objectives.
🧰 Tools
🪛 Pylint (3.3.7)
[convention] 7136-7136: Missing function or method docstring
(C0116)
[warning] 7136-7136: Redefining name 'run' from outer scope (line 41)
(W0621)
There was a problem hiding this comment.
Actionable comments posted: 6
🧹 Nitpick comments (9)
bio/trf/meta.yaml (4)
20-20: Fix typo in parameter description.There's a spelling error in the
extraparameter description.- extra: "Optional command-line flags to pass to Tandem Repeats Finder (TRF). |nl| These flags are appended after the 7 required numeric parameters. Supported flags (default state in parentheses): -m (generate masked sequence file), -f (include flanking sequence), -d (produce .dat file), -h (suppress HTML output), -l <n> (set max tandem repeat size, allowed: >=1, preffered: >=1 and <=29), -ngs (more compact .dat output on multisequence files), -u (usage), -v (version). Provide flags as a quoted string, e.g., '-d -h'." + extra: "Optional command-line flags to pass to Tandem Repeats Finder (TRF). |nl| These flags are appended after the 7 required numeric parameters. Supported flags (default state in parentheses): -m (generate masked sequence file), -f (include flanking sequence), -d (produce .dat file), -h (suppress HTML output), -l <n> (set max tandem repeat size, allowed: >= 1, preferred: >= 1 and <= 29), -ngs (more compact .dat output on multisequence files), -u (usage), -v (version). Provide flags as a quoted string, e.g., '-d -h'."
22-24: Fix formatting and typo in notes section.There are trailing spaces and a typo in the notes section.
notes: > - Flag(s) are specified using the 'extra' param (e.g., '-d -h'). + Flag(s) are specified using the 'extra' param (e.g., '-d -h'). For `-l` flag, write it with space like -l 29. TRF documentation allows -l=29 **but on current version running it behaves - abonormally, hence avoid, as this behaves according to the utility.** |nl| |nl| + abnormally, hence avoid, as this behaves according to the utility.** |nl| |nl|🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 22-22: trailing spaces
(trailing-spaces)
28-28: Fix formatting inconsistency in developer notes.There's an unnecessary period after "For Developers: |nl|".
- For Developers: |nl|. + For Developers: |nl|
36-37: Fix trailing spaces and missing newline.Static analysis identified formatting issues that should be addressed.
|nl| - Note: As this is a wrapper for TRF utility, it comes with it's limitations or defects if any. Also, allowed values mentioned - below are specified as deduced from the TRF's resources, so this wrapper doesn't validate on top of the TRF utility, rather depict's TRF behaviour. + Note: As this is a wrapper for TRF utility, it comes with its limitations or defects if any. Also, allowed values mentioned + below are specified as deduced from the TRF's resources, so this wrapper doesn't validate on top of the TRF utility, rather depicts TRF behaviour. +🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 36-36: trailing spaces
(trailing-spaces)
[error] 37-37: no new line character at the end of file
(new-line-at-end-of-file)
test_wrappers.py (5)
6962-6996: Improve line formatting for better readability.The test logic is excellent and comprehensive, validating multiple TRF output file types. However, the long lines in the
compare_results_with_expecteddictionary should be formatted for better readability.Consider breaking the long dictionary entries across multiple lines:
compare_results_with_expected={ - "trf_output/small_test/" - "small_test.fasta.2.7.7.80.10.50.500.dat": - "expected/small_test.fasta.2.7.7.80.10.50.500.dat", + "trf_output/small_test/small_test.fasta.2.7.7.80.10.50.500.dat": ( + "expected/small_test.fasta.2.7.7.80.10.50.500.dat" + ), - "trf_output/small_test/small_test.fasta.2.7.7.80.10.50.500.mask": - "expected/small_test.fasta.2.7.7.80.10.50.500.mask", + "trf_output/small_test/small_test.fasta.2.7.7.80.10.50.500.mask": ( + "expected/small_test.fasta.2.7.7.80.10.50.500.mask" + ),🧰 Tools
🪛 Pylint (3.3.7)
[convention] 6962-6962: Missing function or method docstring
(C0116)
[warning] 6962-6962: Redefining name 'run' from outer scope (line 41)
(W0621)
6998-7010: Add docstring for better documentation.The test logic is sound for validating parameter order flexibility in TRF. Consider adding a docstring to explain the test purpose.
def test_trf_basic_with_change_order(run): + """Test TRF wrapper with different parameter order and missing extra flags.""" run(🧰 Tools
🪛 Pylint (3.3.7)
[convention] 6998-6998: Missing function or method docstring
(C0116)
[warning] 6998-6998: Redefining name 'run' from outer scope (line 41)
(W0621)
7013-7027: Excellent negative testing approach.The test correctly validates error handling for invalid parameter values using
pytest.raises. This ensures the wrapper properly validates inputs and fails gracefully.Consider adding a docstring:
def test_trf_with_invalid_param_value(run): + """Test that TRF wrapper fails appropriately when required parameter values are missing.""" with pytest.raises(subprocess.CalledProcessError):🧰 Tools
🪛 Pylint (3.3.7)
[convention] 7013-7013: Missing function or method docstring
(C0116)
[warning] 7013-7013: Redefining name 'run' from outer scope (line 41)
(W0621)
7029-7047: Good test coverage for additional flags with formatting improvements needed.The test appropriately validates support for additional permissible flags. The single file comparison might be sufficient for this specific test case.
Apply the same line formatting improvements as suggested for the previous test:
compare_results_with_expected={ - "trf_output/small_test/" - "small_test.fasta.2.7.7.80.10.50.500.dat": - "expected/small_test.fasta.2.7.7.80.10.50.500.dat", + "trf_output/small_test/small_test.fasta.2.7.7.80.10.50.500.dat": ( + "expected/small_test.fasta.2.7.7.80.10.50.500.dat" + ),🧰 Tools
🪛 Pylint (3.3.7)
[convention] 7029-7029: Missing function or method docstring
(C0116)
[warning] 7029-7029: Redefining name 'run' from outer scope (line 41)
(W0621)
7049-7082: Comprehensive case-insensitive parameter testing with formatting needs.Excellent test for validating case-insensitive parameter handling, ensuring the wrapper is user-friendly. The comprehensive output validation is appropriate for this functionality test.
Apply consistent line formatting improvements throughout the dictionary:
compare_results_with_expected={ - "trf_output/small_test/" - "small_test.fasta.2.7.7.80.10.50.500.dat": - "expected/small_test.fasta.2.7.7.80.10.50.500.dat", + "trf_output/small_test/small_test.fasta.2.7.7.80.10.50.500.dat": ( + "expected/small_test.fasta.2.7.7.80.10.50.500.dat" + ),Also consider adding a docstring:
def test_trf_basic_with_uppercase_params(run): + """Test TRF wrapper accepts parameters with uppercase keys and produces correct outputs.""" run(🧰 Tools
🪛 Pylint (3.3.7)
[convention] 7049-7049: Missing function or method docstring
(C0116)
[warning] 7049-7049: Redefining name 'run' from outer scope (line 41)
(W0621)
📜 Review details
Configuration used: CodeRabbit UI
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Plan: Pro
📒 Files selected for processing (7)
bio/trf/environment.linux-64.pin.txt(1 hunks)bio/trf/environment.yaml(1 hunks)bio/trf/meta.yaml(1 hunks)bio/trf/test/Snakefile(1 hunks)bio/trf/test/tests.smk(1 hunks)bio/trf/wrapper.py(1 hunks)test_wrappers.py(5 hunks)
🚧 Files skipped from review as they are similar to previous changes (4)
- bio/trf/environment.yaml
- bio/trf/environment.linux-64.pin.txt
- bio/trf/test/tests.smk
- bio/trf/test/Snakefile
🧰 Additional context used
📓 Path-based instructions (2)
`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
bio/trf/wrapper.pytest_wrappers.py
`**/wrapper.py`: Do not complain about use of undefined variable called `snakemake`.
**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.
bio/trf/wrapper.py
🪛 Ruff (0.11.9)
bio/trf/wrapper.py
70-70: Undefined name snakemake
(F821)
70-70: Undefined name snakemake
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71-71: Undefined name snakemake
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77-77: Undefined name snakemake
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78-78: Undefined name snakemake
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90-90: Undefined name snakemake
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🪛 Pylint (3.3.7)
bio/trf/wrapper.py
[error] 12-12: Unable to import 'snakemake.shell'
(E0401)
[error] 70-70: Undefined variable 'snakemake'
(E0602)
[error] 70-70: Undefined variable 'snakemake'
(E0602)
[error] 71-71: Undefined variable 'snakemake'
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[error] 73-73: Undefined variable 'snakemake'
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[error] 74-74: Undefined variable 'snakemake'
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[error] 77-77: Undefined variable 'snakemake'
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[error] 78-78: Undefined variable 'snakemake'
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[error] 90-90: Undefined variable 'snakemake'
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test_wrappers.py
[convention] 2067-2067: Line too long (162/100)
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[convention] 2118-2118: Line too long (130/100)
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[convention] 6962-6962: Missing function or method docstring
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[warning] 6962-6962: Redefining name 'run' from outer scope (line 41)
(W0621)
[convention] 6998-6998: Missing function or method docstring
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[warning] 6998-6998: Redefining name 'run' from outer scope (line 41)
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[convention] 7013-7013: Missing function or method docstring
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[warning] 7013-7013: Redefining name 'run' from outer scope (line 41)
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[convention] 7029-7029: Missing function or method docstring
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[warning] 7029-7029: Redefining name 'run' from outer scope (line 41)
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[convention] 7049-7049: Missing function or method docstring
(C0116)
[warning] 7049-7049: Redefining name 'run' from outer scope (line 41)
(W0621)
🪛 YAMLlint (1.37.1)
bio/trf/meta.yaml
[error] 22-22: trailing spaces
(trailing-spaces)
[error] 36-36: trailing spaces
(trailing-spaces)
[error] 37-37: no new line character at the end of file
(new-line-at-end-of-file)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: Summary
🔇 Additional comments (2)
bio/trf/wrapper.py (1)
12-12:❌ Incorrect review comment
Missing imports that are referenced in past review comments.
The past review comment mentioned imports from
config,utils.filteration,utils.logger_utils, andutils.validationmodules, but these imports are not present in the current code. However, the AI summary indicates these modules exist in the codebase. This suggests the implementation may be incomplete.
🏁 Script executed:
#!/bin/bash # Description: Check if the referenced modules exist in the codebase and if they should be imported # Check for config module fd -t f "config.py" bio/trf/ fd -t d "config" bio/trf/ # Check for utils modules fd -t d "utils" bio/trf/ fd -t f "*filteration*" bio/trf/ fd -t f "*logger_utils*" bio/trf/ fd -t f "*validation*" bio/trf/ # Check if TRFConfig class is used anywhere rg "TRFConfig" bio/trf/Length of output: 2072
#!/bin/bash # Inspect imports and references in bio/trf/wrapper.py echo "=== Import statements in bio/trf/wrapper.py ===" rg -n "^(import|from)" bio/trf/wrapper.py echo echo "=== References to TRFConfig and utils in bio/trf/wrapper.py ===" rg -n "TRFConfig" bio/trf/wrapper.py || true rg -n "filteration" bio/trf/wrapper.py || true rg -n "logger_utils" bio/trf/wrapper.py || true rg -n "validation" bio/trf/wrapper.py || true
No missing imports in
bio/trf/wrapper.py
A review of the current wrapper shows it only imports and usessnakemake.shell. There are no references toTRFConfigor anyutils.*modules in this file. The past comments about importingconfig,utils.filteration,utils.logger_utils, orutils.validationdo not apply to the current implementation.• Imports found in
wrapper.py
from snakemake.shell import shell• No occurrences of
TRFConfigfilterationlogger_utilsvalidationThe code does not require the previously mentioned imports—please ignore that outdated feedback.
Likely an incorrect or invalid review comment.
🧰 Tools
🪛 Pylint (3.3.7)
[error] 12-12: Unable to import 'snakemake.shell'
(E0401)
test_wrappers.py (1)
2067-2069: LGTM! Good formatting improvements.The addition of explanatory comments for disabled gzip file comparisons and trailing commas improve code readability and maintainability.
Also applies to: 2118-2119
🧰 Tools
🪛 Pylint (3.3.7)
[convention] 2067-2067: Line too long (162/100)
(C0301)
…e-wrappers into add_trf_wrapper
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Nitpick comments (2)
bio/trf/meta.yaml (1)
22-22: Fix formatting issues identified by static analysis.The YAML file has trailing whitespace and is missing a newline at the end of the file.
Apply this diff to fix the formatting:
-notes: > +notes: > - below are specified as deduced from the TRF's resources, so this wrapper doesn't validate on top of the TRF utility, rather depict's TRF behaviour. + below are specified as deduced from the TRF's resources, so this wrapper doesn't validate on top of the TRF utility, rather depict's TRF behaviour. +Also applies to: 36-36, 37-37
🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 22-22: trailing spaces
(trailing-spaces)
bio/trf/wrapper.py (1)
59-59: Optimize dictionary access.Use direct membership testing instead of accessing
.keys()for better performance and readability.Apply this diff:
- k: collected_params[k] for k in trf_params.keys() if k in collected_params + k: collected_params[k] for k in trf_params if k in collected_params🧰 Tools
🪛 Ruff (0.11.9)
59-59: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (2)
bio/trf/meta.yaml(1 hunks)bio/trf/wrapper.py(1 hunks)
🧰 Additional context used
📓 Path-based instructions (2)
`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
bio/trf/wrapper.py
`**/wrapper.py`: Do not complain about use of undefined variable called `snakemake`.
**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.
bio/trf/wrapper.py
🧠 Learnings (1)
bio/trf/wrapper.py (1)
Learnt from: rohan-ibn-tariq
PR: snakemake/snakemake-wrappers#4160
File: bio/trf/wrapper.py:18-26
Timestamp: 2025-06-04T06:32:20.050Z
Learning: For Snakemake wrappers, it's preferable to keep parameter dictionaries and constants directly visible in wrapper.py files rather than importing from config modules, to maintain minimal, self-documenting code that doc viewers can understand at a glance.
🪛 Ruff (0.11.9)
bio/trf/wrapper.py
59-59: Use key in dict instead of key in dict.keys()
Remove .keys()
(SIM118)
76-76: Undefined name snakemake
(F821)
76-76: Undefined name snakemake
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78-78: Undefined name snakemake
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93-93: Undefined name snakemake
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116-116: Undefined name snakemake
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🪛 Pylint (3.3.7)
bio/trf/wrapper.py
[error] 12-12: Unable to import 'snakemake.shell'
(E0401)
[error] 76-76: Undefined variable 'snakemake'
(E0602)
[error] 76-76: Undefined variable 'snakemake'
(E0602)
[error] 78-78: Undefined variable 'snakemake'
(E0602)
[error] 80-80: Undefined variable 'snakemake'
(E0602)
[error] 81-81: Undefined variable 'snakemake'
(E0602)
[error] 92-92: Undefined variable 'snakemake'
(E0602)
[error] 93-93: Undefined variable 'snakemake'
(E0602)
[error] 116-116: Undefined variable 'snakemake'
(E0602)
🪛 YAMLlint (1.37.1)
bio/trf/meta.yaml
[error] 22-22: trailing spaces
(trailing-spaces)
[error] 36-36: trailing spaces
(trailing-spaces)
[error] 37-37: no new line character at the end of file
(new-line-at-end-of-file)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: Summary
🔇 Additional comments (1)
bio/trf/wrapper.py (1)
1-129: Excellent implementation quality with comprehensive error handling.The TRF wrapper implementation demonstrates high quality with:
- Robust parameter validation with clear error messages
- Comprehensive error handling throughout the workflow
- Graceful fallback for logging setup failures
- Well-structured command construction and execution
- Informative user feedback and warnings
The code is well-documented and follows Snakemake wrapper conventions effectively.
🧰 Tools
🪛 Ruff (0.11.9)
59-59: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
76-76: Undefined name
snakemake(F821)
76-76: Undefined name
snakemake(F821)
78-78: Undefined name
snakemake(F821)
80-80: Undefined name
snakemake(F821)
81-81: Undefined name
snakemake(F821)
92-92: Undefined name
snakemake(F821)
93-93: Undefined name
snakemake(F821)
116-116: Undefined name
snakemake(F821)
🪛 Pylint (3.3.7)
[error] 12-12: Unable to import 'snakemake.shell'
(E0401)
[error] 76-76: Undefined variable 'snakemake'
(E0602)
[error] 76-76: Undefined variable 'snakemake'
(E0602)
[error] 78-78: Undefined variable 'snakemake'
(E0602)
[error] 80-80: Undefined variable 'snakemake'
(E0602)
[error] 81-81: Undefined variable 'snakemake'
(E0602)
[error] 92-92: Undefined variable 'snakemake'
(E0602)
[error] 93-93: Undefined variable 'snakemake'
(E0602)
[error] 116-116: Undefined variable 'snakemake'
(E0602)
This PR provides support of executing TRF command line utility (https://prefix.dev/channels/bioconda/packages/trf) through Snakemake using Snakemake wrappers. On top of basic TRF feature(s) this wrapper additionally makes it easy for users to write Snakemake rules by providing following things:
QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefile-> yes, but in test-wrappers.pyinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points to -> Not applicable in my case.meta.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
Tests