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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Extend Functionality to Handle Local Files Based on Tax IDs #50
This PR aims to extend the functionality of the existing process_local_files utility function to handle genomic fasta files based on either species names or tax IDs. The modifications make the function more flexible and robust, paving the way for a more streamlined data processing pipeline.
Changes:
file_utils.py:
Added a new utility function process_local_files that takes an id_type parameter to distinguish between species and tax IDs.
Updated logging messages for better tracking and debugging.
nanometa_prepare.py:
Imported process_local_files from file_utils.
Updated the main() function to call process_local_files for both species and tax ID-based local files.
Removed the species_to_taxid dictionary creation as it was redundant given the species_taxid_dict.
Updated error handling and logging for more clarity.
Summary:
This PR aims to extend the functionality of the existing
process_local_filesutility function to handle genomic fasta files based on either species names or tax IDs. The modifications make the function more flexible and robust, paving the way for a more streamlined data processing pipeline.Changes:
file_utils.py:
process_local_filesthat takes anid_typeparameter to distinguish between species and tax IDs.nanometa_prepare.py:
process_local_filesfromfile_utils.main()function to callprocess_local_filesfor both species and tax ID-based local files.species_to_taxiddictionary creation as it was redundant given thespecies_taxid_dict.