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  • Installation
  • Overview of the Workflows
  • Contents of SPECIMEN
    • specimen subpackages
      • specimen.classes
      • specimen.cmpb
      • specimen.hqtb
      • specimen.util
    • specimen submodules
      • specimen.cmd_access
  • Help & FAQ
  • Notes for Developers
SPECIMEN
  • Contents of SPECIMEN
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Contents of SPECIMEN

The SPECIMEN package contains a number of modules and subpackages, which are listed below.

To search for specific entities by name, use the Index.

For a list of the modules, see Module Index.

specimen subpackages

  • specimen.classes
    • specimen.classes.reports submodule
      • SpecimenModelInfoReport
  • specimen.cmpb
    • specimen.cmpb submodules
      • specimen.cmpb.workflow
  • specimen.hqtb
    • specimen.hqtb subpackages
      • specimen.hqtb.core package
    • specimen.hqtb submodules
      • specimen.hqtb.workflow
  • specimen.util
    • specimen.util submodules
    • specimen.util.set_up module
      • CMPB_CONFIG_PATHS_REQUIRED
      • HQTB_CONFIG_PATH_OPTIONAL
      • HQTB_CONFIG_PATH_REQUIRED
      • PIPELINE_PATHS_OPTIONAL
      • PIPELINE_PATHS_REQUIRED
      • build_data_directories()
      • download_config()
      • save_cmpb_user_input()
      • validate_config()
    • specimen.util.util module
      • create_DIAMOND_db_from_folder()
      • create_NCBIinfo_mapping()

specimen submodules

  • specimen.cmd_access
    • General Options
    • specimen setup
    • specimen hqtb
    • specimen cmpb
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