pdm_utils package

Subpackages

• pdm_utils.classes package
  • Submodules
  • pdm_utils.classes.alchemyhandler module
  • pdm_utils.classes.aragornhandler module
  • pdm_utils.classes.bundle module
  • pdm_utils.classes.cds module
  • pdm_utils.classes.cdspair module
  • pdm_utils.classes.dbcomparesummary module
  • pdm_utils.classes.evaluation module
  • pdm_utils.classes.fileio module
  • pdm_utils.classes.filter module
  • pdm_utils.classes.genome module
  • pdm_utils.classes.genomepair module
  • pdm_utils.classes.genometriad module
  • pdm_utils.classes.randomfieldupdatehandler module
  • pdm_utils.classes.source module
  • pdm_utils.classes.ticket module
  • pdm_utils.classes.tmrna module
  • pdm_utils.classes.trna module
  • pdm_utils.classes.trnascansehandler module
  • Module contents
• pdm_utils.constants package
  • Submodules
  • pdm_utils.constants.constants module
  • pdm_utils.constants.db_schema_0 module
  • pdm_utils.constants.eval_descriptions module
  • pdm_utils.constants.schema_conversions module
  • Module contents
• pdm_utils.functions package
  • Submodules
  • pdm_utils.functions.annotation module
  • pdm_utils.functions.basic module
  • pdm_utils.functions.cartography module
  • pdm_utils.functions.configfile module
  • pdm_utils.functions.eval_modes module
  • pdm_utils.functions.fileio module
  • pdm_utils.functions.flat_files module
  • pdm_utils.functions.mysqldb module
  • pdm_utils.functions.mysqldb_basic module
  • pdm_utils.functions.ncbi module
  • pdm_utils.functions.parallelize module
  • pdm_utils.functions.parsing module
  • pdm_utils.functions.phagesdb module
  • pdm_utils.functions.phameration module
  • pdm_utils.functions.pipelines_basic module
  • pdm_utils.functions.querying module
  • pdm_utils.functions.server module
  • pdm_utils.functions.tickets module
  • Module contents
• pdm_utils.pipelines package
  • Submodules
  • pdm_utils.pipelines.compare_db module
  • pdm_utils.pipelines.convert_db module
  • pdm_utils.pipelines.email_submitters module
  • pdm_utils.pipelines.export_db module
  • pdm_utils.pipelines.find_domains module
  • pdm_utils.pipelines.freeze_db module
  • pdm_utils.pipelines.get_data module
  • pdm_utils.pipelines.get_db module
  • pdm_utils.pipelines.get_gb_records module
  • pdm_utils.pipelines.import_genome module
  • pdm_utils.pipelines.pham_finder module
  • pdm_utils.pipelines.phamerate module
  • pdm_utils.pipelines.push_db module
  • pdm_utils.pipelines.review module
  • pdm_utils.pipelines.revise module
  • pdm_utils.pipelines.update_field module
  • Module contents

Submodules

pdm_utils.run module

Use this script to run all pipelines within the pipelines folder. It verifies a valid pipeline is selected, then passes all command line arguments to the main pipeline module.

pdm_utils.run.main(unparsed_args)

Run a pdm_utils pipeline.

pdm_utils.run.parse_args(unparsed_args)

Use argparse to verify pipeline argument only.

Parameters

unparsed_args (list) – raw command line args

Module contents