Add PlasmidFinder module and integration instructions for Kleborate#112
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tnmquann wants to merge 3 commits intoklebgenomics:mainfrom
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Add PlasmidFinder module and integration instructions for Kleborate#112tnmquann wants to merge 3 commits intoklebgenomics:mainfrom
tnmquann wants to merge 3 commits intoklebgenomics:mainfrom
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- Implemented general__plasmidfinder.py to integrate PlasmidFinder for detecting plasmid replicons. - Added command-line options for custom configurations including database path, minimum coverage, and identity threshold. - Created functions for handling input files, running PlasmidFinder, and parsing its JSON output. - Developed unit tests for module functionality, including CLI option validation and output parsing. - Included a sample data.json file for testing purposes. - Removed obsolete download.sh script.
Added comprehensive installation and usage instructions for the PlasmidFinder module within Kleborate 3, including prerequisites, installation steps, usage examples, and troubleshooting tips.
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Pull request overview
This pull request adds a new general__plasmidfinder module to run PlasmidFinder within Kleborate, along with user-facing integration documentation and example JSON output for tests.
Changes:
- Introduces a new Kleborate module (
general__plasmidfinder) that runsplasmidfinder.py, parsesdata.json, and optionally copies extended outputs into{outdir}/{strain}/. - Adds a comprehensive module-specific usage guide (
instructions.md) for installation, parameters, workflows, outputs, and troubleshooting. - Adds unit/integration-style tests plus realistic sample PlasmidFinder JSON output (
test_files/data.json) to validate parsing and expected result structure.
Reviewed changes
Copilot reviewed 4 out of 7 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
kleborate/modules/general__plasmidfinder/general__plasmidfinder.py |
New module implementation (CLI options, external program check, PlasmidFinder invocation, JSON parsing, extended output copying). |
kleborate/modules/general__plasmidfinder/test_general__plasmidfinder.py |
New test suite covering CLI validation, parsing behavior, and optional integration tests. |
kleborate/modules/general__plasmidfinder/test_files/data.json |
Sample PlasmidFinder JSON output used by parsing tests. |
kleborate/modules/general__plasmidfinder/data/instructions.md |
End-user documentation for installing and running the module (and interpreting outputs). |
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Collaborator
|
Hi @tnmquann thanks for contributing this! |
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This pull request introduces PlasmidFinder module with Kleborate 3. The documentation covers installation, usage, parameter mapping, output interpretation, troubleshooting, and example workflows. The test data file provides a sample result structure for validating PlasmidFinder integration.
Documentation and User Guide:
instructions.mdtogeneral__plasmidfinderdirectory, covering installation, usage, parameter mapping, example workflows, output interpretation, troubleshooting, and related resources for running PlasmidFinder within Kleborate 3.Test Data:
data.jsontogeneral__plasmidfinder/test_files, providing example PlasmidFinder output with realistic test results for Enterobacteriaceae and Gram Positive categories, including hit details and run metadata.