A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline functionality post-initialization.
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Enhancements in nanometa-prepare for Improved Usability and Flexibility #49
This PR introduces several key enhancements and fixes to improve the functionality and flexibility of the nanometa_live package. The primary focus is on the introduction of different operational modes for handling genome files and more flexible data types for updating YAML configuration files.
Changes
config_utils.py: Enhanced update_yaml_config_with_taxid to accept either a DataFrame or a dictionary as input. This allows for greater flexibility when working with different data types.
kraken_utils.py: Extended parse_kraken2_inspect to optionally filter the output based on a provided species list. This provides more focused data when needed.
nanometa_prepare.py: Introduced a new argument --mode to choose the operational mode for handling genome files. The script now also checks if the selected mode is implemented yet, and exits with an error message if it's not. Further modularized code for better readability and maintainability.
Further Details
Flexible YAML Configuration Update: The function update_yaml_config_with_taxid now supports updating the YAML configuration file using either a DataFrame or a dictionary, making it easier to use in different contexts.
Species Filtering in Kraken2 Parsing: The function parse_kraken2_inspect now accepts an optional species_list argument to filter the output, allowing for more targeted data retrieval.
Operational Modes: A new command-line argument --mode has been added to nanometa_prepare.py to allow the user to specify the operational mode for handling genome files. Currently supported mode is 'gtdb-api', with placeholders for future modes like 'gtdb-file', 'local-species', and 'local-taxid'.
Code Modularization: nanometa_prepare.py has been refactored for improved readability and maintainability. This will make it easier to add new features and modes in the future.
Impact
These changes improve the package's flexibility and make it more robust, setting the foundation for future features and improvements.
This PR introduces several key enhancements and fixes to improve the functionality and flexibility of the
nanometa_livepackage. The primary focus is on the introduction of different operational modes for handling genome files and more flexible data types for updating YAML configuration files.Changes
config_utils.py: Enhancedupdate_yaml_config_with_taxidto accept either a DataFrame or a dictionary as input. This allows for greater flexibility when working with different data types.kraken_utils.py: Extendedparse_kraken2_inspectto optionally filter the output based on a provided species list. This provides more focused data when needed.nanometa_prepare.py: Introduced a new argument--modeto choose the operational mode for handling genome files. The script now also checks if the selected mode is implemented yet, and exits with an error message if it's not. Further modularized code for better readability and maintainability.Further Details
Flexible YAML Configuration Update: The function
update_yaml_config_with_taxidnow supports updating the YAML configuration file using either a DataFrame or a dictionary, making it easier to use in different contexts.Species Filtering in Kraken2 Parsing: The function
parse_kraken2_inspectnow accepts an optionalspecies_listargument to filter the output, allowing for more targeted data retrieval.Operational Modes: A new command-line argument
--modehas been added tonanometa_prepare.pyto allow the user to specify the operational mode for handling genome files. Currently supported mode is 'gtdb-api', with placeholders for future modes like 'gtdb-file', 'local-species', and 'local-taxid'.Code Modularization:
nanometa_prepare.pyhas been refactored for improved readability and maintainability. This will make it easier to add new features and modes in the future.Impact
These changes improve the package's flexibility and make it more robust, setting the foundation for future features and improvements.