Enhance Nanopore Simulator: Improve Filename Handling and Error Management

[druvus]

Description

This pull request introduces several key enhancements to the nanopore_simulator.py script:

• Filename Handling:

  • Resolved Duplicate Extensions: Fixed the issue of output filenames having duplicate .fastq extensions (e.g., demo.fastq.fastq.gz) by implementing a get_base_name function to extract the correct base name.
  • Prefix Customization: Added a --prefix argument allowing users to specify custom prefixes for output filenames, enhancing flexibility and organization.

• Delay Management:

  • Integer Delays: Modified delay intervals to use integer seconds instead of floating-point numbers, ensuring consistent and predictable wait times between operations.

• Error Handling and Validation:

  • Enhanced Argument Validation: Implemented thorough checks for command-line arguments to ensure they meet required criteria (e.g., non-negative delays, positive read counts).
  • Robust Exception Handling: Added granular exception handling to provide informative error messages and prevent unexpected script crashes.

• Code Refactoring:

  • Modular Functions: Refactored the script to improve modularity and readability, making it easier to maintain and extend.
  • Logging Enhancements: Updated logging configuration to include StreamHandler for real-time console output and added debug logs for better traceability.

Key Changes

• Added a helper function get_base_name to accurately extract file base names without suffixes.
• Updated copy_files_simulation and subsample_reads_simulation functions to incorporate prefix handling and prevent filename duplication.
• Changed delay generation from floating-point to integer seconds using random.randint.
• Enhanced command-line argument parsing with additional validations and the new --prefix option.
• Improved logging setup for better visibility and debugging capabilities.