specimen.hqtb package

This subspacke contains everything for the HQTB pipeline.

specimen.hqtb subpackages

• specimen.hqtb.core package
  • specimen.hqtb.core.refinement subpackage
    • specimen.hqtb.core.refinement.annotation submodule
    • specimen.hqtb.core.refinement.cleanup submodule
    • specimen.hqtb.core.refinement.extension submodule
    • specimen.hqtb.core.refinement.smoothing submodule
  • specimen.hqtb.core submodules
    • specimen.hqtb.core.analysis
      • run()
    • specimen.hqtb.core.bidirectional_blast
      • bdbp_diamond()
      • create_diamond_db()
      • extract_bestbdbp_hits()
      • extract_cds()
      • run()
      • run_diamond_blastp()
    • specimen.hqtb.core.generate_draft_model
      • check_unchanged()
      • edit_template_identifiers()
      • gen_draft_model()
      • pid_filter()
      • remove_absent_genes()
      • rename_found_homologs()
      • run()
    • specimen.hqtb.core.validation
      • run()

specimen.hqtb submodules

specimen.hqtb.workflow

Functions to run the workflow to create a GEM based on a high-quality template model.

specimen.hqtb.workflow.run(config_file: str = 'test_config.yaml')

Run the complete workflow for creating a strain-specific model.

Args:

• config_file (str, optional):

  Path to the config file. Defaults to ‘test_config.yaml’.

Raises:

• ValueError: Unkown file extension.

specimen.hqtb.workflow.wrapper(config_file: str, parent_dir: str = '')

Run the pipeline multiple times on a folder containing subfolders with subject annotated genomes and full genome sequences using the same configuration.

Args:

• config_file (str):

  config file containing the general information to run the pipeline. The information for the subject and output place/name can be empty.

• parent_dir (str, optional):

  Path to a directory to search for subfolders containing the data. Defaults to “”.

Raises:

• ValueError: No or multiple annotated genome files found: subfolder

• ValueError: No or multiple full genome files found: subfolder