Index

C

cagecleaner.communication module cagecleaner.file_utils module cagecleaner.genome_run module cagecleaner.local_genome_run module cagecleaner.local_region_run module cagecleaner.local_run module cagecleaner.main module

cagecleaner.region_run module cagecleaner.remote_genome_run module cagecleaner.remote_region_run module cagecleaner.remote_run module cagecleaner.run module cagecleaner.utils module convert_genbanks_to_fastas() (in module cagecleaner.file_utils) correct_layouts() (in module cagecleaner.utils) create_parser() (in module cagecleaner.main)

D

dereplicate_genomes() (cagecleaner.genome_run.GenomeRun method)

dereplicate_regions() (cagecleaner.region_run.RegionRun method) download_regions() (in module cagecleaner.communication)

E

extract_regions() (cagecleaner.local_region_run.LocalRegionRun method)

F

fetch_assembly_ids() (cagecleaner.remote_genome_run.RemoteGenomeRun method) fetch_contig_lengths() (in module cagecleaner.communication)

fetch_genomes() (cagecleaner.remote_genome_run.RemoteGenomeRun method) fetch_regions() (cagecleaner.remote_region_run.RemoteRegionRun method) filter_session() (cagecleaner.run.Run method)

G

generate_cblaster_session() (in module cagecleaner.utils) generate_output() (cagecleaner.run.Run method)

GenomeRun (class in cagecleaner.genome_run) get_assembly_accessions() (in module cagecleaner.communication)

I

initialise_binary() (cagecleaner.run.Run method)

is_fasta() (in module cagecleaner.file_utils) is_genbank() (in module cagecleaner.file_utils)

J

join_assemblies_with_binary() (cagecleaner.remote_genome_run.RemoteGenomeRun method) join_dereplication_with_binary() (cagecleaner.local_genome_run.LocalGenomeRun method) (cagecleaner.local_region_run.LocalRegionRun method) (cagecleaner.local_run.LocalRun method) (cagecleaner.remote_genome_run.RemoteGenomeRun method) (cagecleaner.remote_region_run.RemoteRegionRun method) (cagecleaner.remote_run.RemoteRun method) (cagecleaner.run.Run method)

L

LocalGenomeRun (class in cagecleaner.local_genome_run)

LocalRegionRun (class in cagecleaner.local_region_run) LocalRun (class in cagecleaner.local_run)

M

main() (in module cagecleaner.main) map_scaffolds_to_assemblies() (cagecleaner.remote_genome_run.RemoteGenomeRun method) module cagecleaner.communication cagecleaner.file_utils cagecleaner.genome_run cagecleaner.local_genome_run cagecleaner.local_region_run cagecleaner.local_run cagecleaner.main cagecleaner.region_run cagecleaner.remote_genome_run cagecleaner.remote_region_run cagecleaner.remote_run cagecleaner.run cagecleaner.utils

P

prepare_genomes() (cagecleaner.local_run.LocalRun method)

R

recover_hits() (cagecleaner.run.Run method) RegionRun (class in cagecleaner.region_run) RemoteGenomeRun (class in cagecleaner.remote_genome_run) RemoteRegionRun (class in cagecleaner.remote_region_run) RemoteRun (class in cagecleaner.remote_run) remove_suffixes() (in module cagecleaner.file_utils)

Run (class in cagecleaner.run) run() (cagecleaner.local_genome_run.LocalGenomeRun method) (cagecleaner.local_region_run.LocalRegionRun method) (cagecleaner.remote_genome_run.RemoteGenomeRun method) (cagecleaner.remote_region_run.RemoteRegionRun method) (cagecleaner.run.Run method) run_command() (in module cagecleaner.utils)

S

setup_logging() (in module cagecleaner.main)