assnake.cli package

Subpackages

• assnake.cli.commands package
  • Submodules
  • assnake.cli.commands.cmd_run module
  • assnake.cli.commands.commands_assembly module
  • assnake.cli.commands.dataset_commands module
  • assnake.cli.commands.download_data_command module
  • assnake.cli.commands.init module
  • Module contents

Submodules

assnake.cli.assnake_cli module

assnake.cli.assnake_cli.main()

assnake.cli.import_samples_to_df module

assnake.cli.import_samples_to_df.find_files(base, pattern)

Return list of files matching pattern in base folder.

assnake.cli.import_samples_to_df.get_sample_dict_from_dir(loc, sample, variant, ext)

assnake.cli.import_samples_to_df.get_samples_from_dir(loc)

Searches for samples in loc. Sample should contain R1 and R2 :param loc: location on filesystem where we should search :return: Returns sample dict in loc

assnake.cli.import_samples_to_df.main()

Module contents