Index

C

CAGEcleanerDefaultConfiguration (class in csuite.defaults) categorise_args() (in module csuite.argument_parsers) cblasterMakedbDefaultConfiguration (class in csuite.defaults) cblasterSearchDefaultConfiguration (class in csuite.defaults) cfoldseekerCDSDefaultConfiguration (class in csuite.defaults) cfoldseekerDefaultConfiguration (class in csuite.defaults) create_main_parser() (in module csuite.main) csuite.argument_parsers module

csuite.cli_parsers module csuite.defaults module csuite.main module csuite.validators module csuite.workflows module

E

extractDefaultConfiguration (class in csuite.defaults)

M

main() (in module csuite.main) mainDefaultConfiguration (class in csuite.defaults) module csuite.argument_parsers csuite.cli_parsers csuite.defaults csuite.main csuite.validators csuite.workflows

P

parse_and_validate_args() (in module csuite.argument_parsers)

R

register_derep_subparser() (in module csuite.cli_parsers) register_local_extract_subparser() (in module csuite.cli_parsers) register_local_seq_derep_subparser() (in module csuite.cli_parsers) register_local_seq_subparser() (in module csuite.cli_parsers) register_local_struc_derep_subparser() (in module csuite.cli_parsers) register_local_struc_subparser() (in module csuite.cli_parsers) register_remote_extract_subparser() (in module csuite.cli_parsers) register_remote_seq_derep_subparser() (in module csuite.cli_parsers) register_remote_seq_subparser() (in module csuite.cli_parsers) register_remote_struc_derep_subparser() (in module csuite.cli_parsers) register_remote_struc_subparser() (in module csuite.cli_parsers) register_report_subparser() (in module csuite.cli_parsers) reportDefaultConfiguration (class in csuite.defaults)

run_derep_workflow() (in module csuite.workflows) run_local_extract_workflow() (in module csuite.workflows) run_local_seq_derep_workflow() (in module csuite.workflows) run_local_seq_workflow() (in module csuite.workflows) run_local_struc_derep_workflow() (in module csuite.workflows) run_local_struc_workflow() (in module csuite.workflows) run_remote_extract_workflow() (in module csuite.workflows) run_remote_seq_derep_workflow() (in module csuite.workflows) run_remote_seq_workflow() (in module csuite.workflows) run_remote_struc_derep_workflow() (in module csuite.workflows) run_remote_struc_workflow() (in module csuite.workflows) run_report_workflow() (in module csuite.workflows) run_workflow() (in module csuite.workflows)

S

setup_derep() (in module csuite.workflows) setup_local_extract() (in module csuite.workflows) setup_local_seq() (in module csuite.workflows) setup_local_seq_derep() (in module csuite.workflows) setup_local_struc() (in module csuite.workflows) setup_local_struc_derep() (in module csuite.workflows) setup_logging() (in module csuite.main)

setup_remote_extract() (in module csuite.workflows) setup_remote_seq() (in module csuite.workflows) setup_remote_seq_derep() (in module csuite.workflows) setup_remote_struc() (in module csuite.workflows) setup_remote_struc_derep() (in module csuite.workflows) setup_report() (in module csuite.workflows) setup_workflow() (in module csuite.workflows)

V

validate_cblaster_makedb_args() (in module csuite.validators) validate_cblaster_search_args() (in module csuite.validators)

validate_remote_extract_args() (in module csuite.validators) validate_report_args() (in module csuite.validators)