Index

_

__call__() (macsypy.system.MetaSetOfHits method) __contains__() (macsypy.cluster.Cluster method) (macsypy.database.RepliconDB method) (macsypy.gene.GeneBank method) (macsypy.model.ModelBank method) __delattr__() (macsypy.hit.HitWeight method) (macsypy.scripts.macsyconfig.Theme method) __eq__() (macsypy.hit.CoreHit method) (macsypy.hit.HitWeight method) (macsypy.hit.ModelHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation method) (macsypy.scripts.macsyconfig.Theme method) (macsypy.scripts.macsyprofile.LightHit method) (macsypy.solution.Solution method) __getitem__() (macsypy.database.RepliconDB method) (macsypy.gene.GeneBank method) (macsypy.model.ModelBank method) (macsypy.registries.ModelRegistry method) __gt__() (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation method) (macsypy.solution.Solution method) __hash__ (macsypy.registries.ModelLocation attribute) (macsypy.scripts.macsyprofile.LightHit attribute) (macsypy.solution.Solution attribute) __hash__() (macsypy.gene.CoreGene method) (macsypy.gene.ModelGene method) (macsypy.hit.CoreHit method) (macsypy.hit.HitWeight method) (macsypy.hit.ModelHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) (macsypy.scripts.macsyconfig.Theme method) __init__() (macsypy.cluster.Cluster method) (macsypy.config.Config method) (macsypy.config.MacsyDefaults method) (macsypy.database.Indexes method) (macsypy.database.RepliconDB method) (macsypy.definition_parser.DefinitionParser method) (macsypy.gene.CoreGene method) (macsypy.gene.Exchangeable method) (macsypy.gene.GeneBank method) (macsypy.gene.ModelGene method) (macsypy.hit.AbstractCounterpartHit method) (macsypy.hit.CoreHit method) (macsypy.hit.HitWeight method) (macsypy.hit.Loner method) (macsypy.hit.LonerMultiSystem method) (macsypy.hit.ModelHit method) (macsypy.hit.MultiSystem method) (macsypy.model.Model method) (macsypy.model.ModelBank method) (macsypy.model_conf_parser.ModelConfParser method) (macsypy.package.AbstractModelIndex method) (macsypy.package.LocalModelIndex method) (macsypy.package.Package method) (macsypy.package.RemoteModelIndex method) (macsypy.profile.Profile method) (macsypy.profile.ProfileFactory method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation method) (macsypy.registries.ModelRegistry method) (macsypy.report.HMMReport method) (macsypy.scripts.macsyconfig.Theme method) (macsypy.scripts.macsyprofile.HmmProfile method) (macsypy.scripts.macsyprofile.LightHit method) (macsypy.serialization.TsvSolutionSerializer method) (macsypy.solution.Solution method) (macsypy.system.AbstractClusterizedHits method) (macsypy.system.AbstractSetOfHits method) (macsypy.system.AbstractUnordered method) (macsypy.system.HitSystemTracker method) (macsypy.system.MatchMaker method) (macsypy.system.OrderedMatchMaker method) (macsypy.system.RejectedCandidate method) (macsypy.system.System method) (macsypy.system.UnlikelySystem method) __iter__() (macsypy.database.Indexes method) (macsypy.gene.GeneBank method) (macsypy.model.ModelBank method) (macsypy.solution.Solution method) __len__() (macsypy.model.ModelBank method) (macsypy.profile.Profile method) __lt__() (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation method) (macsypy.solution.Solution method) __new__() (macsypy.package.AbstractModelIndex static method) __repr__() (macsypy.hit.HitWeight method) (macsypy.scripts.macsyconfig.Theme method) (macsypy.scripts.macsyprofile.LightHit method) __setattr__() (macsypy.hit.HitWeight method) (macsypy.scripts.macsyconfig.Theme method) __str__() (macsypy.cluster.Cluster method) (macsypy.gene.ModelGene method) (macsypy.hit.AbstractCounterpartHit method) (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) (macsypy.model.Model method) (macsypy.profile.Profile method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation method) (macsypy.registries.ModelRegistry method) (macsypy.report.HMMReport method) (macsypy.scripts.macsyprofile.LightHit method) (macsypy.system.LikelySystem method) (macsypy.system.RejectedCandidate method) (macsypy.system.UnlikelySystem method)

__weakref__ (macsypy.cluster.Cluster attribute) (macsypy.config.Config attribute) (macsypy.config.MacsyDefaults attribute) (macsypy.config.NoneConfig attribute) (macsypy.database.Indexes attribute) (macsypy.database.RepliconDB attribute) (macsypy.definition_parser.DefinitionParser attribute) (macsypy.error.MacsypyError attribute) (macsypy.gene.CoreGene attribute) (macsypy.gene.GeneBank attribute) (macsypy.gene.ModelGene attribute) (macsypy.hit.CoreHit attribute) (macsypy.hit.HitWeight attribute) (macsypy.hit.ModelHit attribute) (macsypy.model.Model attribute) (macsypy.model.ModelBank attribute) (macsypy.model_conf_parser.ModelConfParser attribute) (macsypy.package.AbstractModelIndex attribute) (macsypy.package.Package attribute) (macsypy.profile.Profile attribute) (macsypy.profile.ProfileFactory attribute) (macsypy.registries.DefinitionLocation attribute) (macsypy.registries.ModelLocation attribute) (macsypy.registries.ModelRegistry attribute) (macsypy.report.HMMReport attribute) (macsypy.scripts.macsyconfig.Theme attribute) (macsypy.scripts.macsyprofile.HmmProfile attribute) (macsypy.scripts.macsyprofile.LightHit attribute) (macsypy.serialization.SystemSerializer attribute) (macsypy.serialization.TsvRejectedCandidatesSerializer attribute) (macsypy.serialization.TsvSolutionSerializer attribute) (macsypy.serialization.TsvSpecialHitSerializer attribute) (macsypy.solution.Solution attribute) (macsypy.system.AbstractSetOfHits attribute) (macsypy.system.HitSystemTracker attribute) (macsypy.system.MatchMaker attribute) _build_my_db() (macsypy.report.HMMReport method) (macsypy.scripts.macsyprofile.HmmProfile method) _build_my_indexes() (macsypy.database.Indexes method) _check_metadata() (macsypy.package.Package method) _check_model_conf() (macsypy.package.Package method) _check_model_consistency() (macsypy.package.Package method) _check_replicon_consistency() (macsypy.cluster.Cluster method) _check_structure() (macsypy.package.Package method) _check_syntax() (macsypy.definition_parser.DefinitionParser method) _config_file_2_dict() (macsypy.config.Config method) _create_exchangeable_map() (macsypy.system.MatchMaker method) _create_model() (macsypy.definition_parser.DefinitionParser method) _fill_gembase_min_max() (macsypy.database.RepliconDB method) _fill_gene_bank() (macsypy.definition_parser.DefinitionParser method) _fill_my_db() (macsypy.report.HMMReport method) (macsypy.scripts.macsyprofile.HmmProfile method) _fill_ordered_min_max() (macsypy.database.RepliconDB method) _fill_topology() (macsypy.database.RepliconDB method) _find_all_installed_packages() (in module macsypy.scripts.macsydata) _find_installed_package() (in module macsypy.scripts.macsydata) _find_readme() (macsypy.package.Package method) _get_model_conf_node() (macsypy.model_conf_parser.ModelConfParser method) _get_model_node() (macsypy.definition_parser.DefinitionParser method) _get_replicon_name() (macsypy.report.GembaseHMMReport method) (macsypy.report.GeneralHMMReport method) (macsypy.report.HMMReport method) (macsypy.report.OrderedHMMReport method) _hit_start() (macsypy.report.HMMReport method) (macsypy.scripts.macsyprofile.HmmProfile method) _index_dir() (macsypy.database.Indexes method) _load_metadata() (macsypy.package.Package method) _loner_warning() (in module macsypy.scripts.macsyfinder) _outfile_header() (in module macsypy.scripts.macsyfinder) _parse_exchangeable() (macsypy.definition_parser.DefinitionParser method) _parse_genes() (macsypy.definition_parser.DefinitionParser method) _parse_hmm_body() (macsypy.report.HMMReport method) (macsypy.scripts.macsyprofile.HmmProfile method) _parse_hmm_header() (macsypy.report.HMMReport method) (macsypy.scripts.macsyprofile.HmmProfile method) _parse_section() (macsypy.model_conf_parser.ModelConfParser method) _profile_features() (macsypy.profile.Profile method) _scan_definitions() (macsypy.registries.ModelLocation method) _scan_profiles() (macsypy.registries.ModelLocation method) _search_in_desc() (in module macsypy.scripts.macsydata) _search_in_ordered_replicon() (in module macsypy.scripts.macsyfinder) _search_in_pack_name() (in module macsypy.scripts.macsydata) _search_in_unordered_replicon() (in module macsypy.scripts.macsyfinder) _set_command_line_config() (macsypy.config.Config method) _set_db_type() (macsypy.config.Config method) _set_default_config() (macsypy.config.Config method) _set_inter_gene_max_space() (macsypy.config.Config method) _set_log_level() (macsypy.config.Config method) _set_max_nb_genes() (macsypy.config.Config method) _set_min_genes_required() (macsypy.config.Config method) _set_min_mandatory_genes_required() (macsypy.config.Config method) _set_model_config() (macsypy.config.Config method) _set_models() (macsypy.config.Config method) _set_models_dir() (macsypy.config.Config method) _set_multi_loci() (macsypy.config.Config method) _set_no_cut_ga() (macsypy.config.Config method) _set_options() (macsypy.config.Config method) _set_previous_run_config() (macsypy.config.Config method) _set_project_config_file() (macsypy.config.Config method) _set_replicon_topology() (macsypy.config.Config method) _set_sequence_db() (macsypy.config.Config method) _set_system_models_dir() (macsypy.config.Config method) _set_system_wide_config() (macsypy.config.Config method) _set_topology_file() (macsypy.config.Config method) _set_user_config_file() (macsypy.config.Config method) _set_user_wide_config() (macsypy.config.Config method) _sorted_systems() (macsypy.solution.Solution method) _str_2_tuple() (macsypy.config.Config method) _url_json() (macsypy.package.RemoteModelIndex method)

A

AbstractClusterizedHits (class in macsypy.system) AbstractCounterpartHit (class in macsypy.hit) AbstractModelIndex (class in macsypy.package) AbstractSetOfHits (class in macsypy.system) AbstractUnordered (class in macsypy.system) accessory_hits (macsypy.system.AbstractUnordered property) add() (macsypy.registries.ModelRegistry method) add_comment() (macsypy.scripts.macsyconfig.ConfigParserWithComments method) add_exchangeable() (macsypy.gene.Exchangeable method) (macsypy.gene.ModelGene method)

add_model() (macsypy.model.ModelBank method) add_new_gene() (macsypy.gene.GeneBank method) add_subdefinition() (macsypy.registries.DefinitionLocation method) all() (macsypy.registries.DefinitionLocation method) allowed_hits (macsypy.system.AbstractUnordered property) alternate_of() (macsypy.gene.Exchangeable method) (macsypy.gene.ModelGene method) ask() (in module macsypy.scripts.macsyconfig) average_wholeness (macsypy.solution.Solution property)

B

best_hit() (macsypy.report.HMMReport method) build() (macsypy.database.Indexes method)

build_arg_parser() (in module macsypy.scripts.macsydata) build_clusters() (in module macsypy.cluster)

C

check() (macsypy.package.Package method) check_bool() (in module macsypy.scripts.macsyconfig) check_choice() (in module macsypy.scripts.macsyconfig) check_consistency() (macsypy.definition_parser.DefinitionParser method) check_dir() (in module macsypy.scripts.macsyconfig) check_exe() (in module macsypy.scripts.macsyconfig) check_file() (in module macsypy.scripts.macsyconfig) check_float() (in module macsypy.scripts.macsyconfig) check_positive_int() (in module macsypy.scripts.macsyconfig) check_str() (in module macsypy.scripts.macsyconfig) CITATION.yml Cluster (class in macsypy.cluster) cmd_name() (in module macsypy.scripts.macsydata)

combine_clusters() (in module macsypy.solution) combine_multisystems() (in module macsypy.solution) compute_best_MSHit() (in module macsypy.hit) Config (class in macsypy.config) ConfigParserWithComments (class in macsypy.scripts.macsyconfig) CONTRIBUTING CONTRIBUTORS COPYING COPYRIGHT core_gene (macsypy.gene.ModelGene property) CoreGene (class in macsypy.gene) CoreHit (class in macsypy.hit) count() (macsypy.system.AbstractSetOfHits method) counterpart (macsypy.hit.AbstractCounterpartHit property)

D

DefinitionLocation (class in macsypy.registries) DefinitionParser (class in macsypy.definition_parser) do_available() (in module macsypy.scripts.macsydata) do_check() (in module macsypy.scripts.macsydata) do_cite() (in module macsypy.scripts.macsydata) do_download() (in module macsypy.scripts.macsydata) do_freeze() (in module macsypy.scripts.macsydata) do_help() (in module macsypy.scripts.macsydata)

do_info() (in module macsypy.scripts.macsydata) do_init_package() (in module macsypy.scripts.macsydata) do_install() (in module macsypy.scripts.macsydata) do_list() (in module macsypy.scripts.macsydata) do_search() (in module macsypy.scripts.macsydata) do_show_definition() (in module macsypy.scripts.macsydata) do_uninstall() (in module macsypy.scripts.macsydata) doc download() (macsypy.package.RemoteModelIndex method)

E

epilog() (in module macsypy.scripts.macsyconfig) Exchangeable (class in macsypy.gene)

exchangeables (macsypy.gene.ModelGene property) execute() (macsypy.profile.Profile method) extract() (macsypy.report.HMMReport method)

F

family_name (macsypy.model.Model property) (macsypy.registries.DefinitionLocation property) fasta_iter() (in module macsypy.database) filter() (macsypy.model.Model method)

find_best_solutions() (in module macsypy.solution) find_my_indexes() (macsypy.database.Indexes method) forbidden_hits (macsypy.system.AbstractUnordered property) fulfilled_function() (macsypy.cluster.Cluster method) (macsypy.system.AbstractClusterizedHits method)

G

GembaseHMMReport (class in macsypy.report) GeneBank (class in macsypy.gene) GeneralHMMReport (class in macsypy.report) genes (macsypy.database.RepliconInfo attribute) genes() (macsypy.model.Model method) genes_fqn() (macsypy.gene.GeneBank method) GeneStatus (class in macsypy.gene) get() (macsypy.database.RepliconDB method) get_all_definitions() (macsypy.registries.ModelLocation method) get_best_hit_4_func() (in module macsypy.hit) get_best_hits() (in module macsypy.hit) get_def_to_detect() (in module macsypy.utils) get_definition() (macsypy.registries.ModelLocation method) get_definitions() (macsypy.registries.ModelLocation method) get_gene() (macsypy.model.Model method)

get_gene_name() (in module macsypy.scripts.macsyprofile) get_hits_encoding_multisystem() (macsypy.system.System method) get_loners() (macsypy.system.System method) get_metadata() (macsypy.package.RemoteModelIndex method) get_multisystems() (macsypy.system.System method) get_position() (macsypy.hit.CoreHit method) get_profile() (macsypy.profile.ProfileFactory method) (macsypy.registries.ModelLocation method) get_profile_len() (in module macsypy.scripts.macsyprofile) get_profiles_names() (macsypy.registries.ModelLocation method) get_replicon_names() (in module macsypy.utils) get_version_message() (in module macsypy.scripts.macsydata) (in module macsypy.scripts.macsyfinder) (in module macsypy.scripts.macsyprofile) getter_maker() (macsypy.system.MetaSetOfHits method) guess_if_really_gembase() (macsypy.database.RepliconDB method)

H

header() (in module macsypy.scripts.macsyprofile) help() (macsypy.package.Package method) hit (macsypy.hit.ModelHit property) hit_weights (macsypy.cluster.Cluster property) hit_weights() (macsypy.config.Config method) hits (macsypy.system.AbstractUnordered property) (macsypy.system.RejectedCandidate property) (macsypy.system.System property)

hits_number (macsypy.solution.Solution property) hits_positions (macsypy.solution.Solution property) HitSystemTracker (class in macsypy.system) HitWeight (class in macsypy.hit) hmmer_dir() (macsypy.config.Config method) HmmProfile (class in macsypy.scripts.macsyprofile) HMMReport (class in macsypy.report)

I

Indexes (class in macsypy.database) info() (macsypy.package.Package method) init_logger() (in module macsypy.scripts.macsydata) (in module macsypy.scripts.macsyprofile) inter_gene_max_space (macsypy.gene.ModelGene property) (macsypy.model.Model property) inter_gene_max_space() (macsypy.config.Config method)

is_accessory() (macsypy.gene.ModelGene method) is_compatible() (macsypy.system.System method) is_exchangeable (macsypy.gene.Exchangeable property) (macsypy.gene.ModelGene property) is_forbidden() (macsypy.gene.ModelGene method) is_mandatory() (macsypy.gene.ModelGene method) items() (macsypy.database.RepliconDB method) iteritems() (macsypy.database.RepliconDB method)

J

join_def_path() (in module macsypy.registries)

L

LightHit (class in macsypy.scripts.macsyprofile) likely_systems_to_tsv() (in module macsypy.scripts.macsyfinder) likely_systems_to_txt() (in module macsypy.scripts.macsyfinder) LikelySystem (class in macsypy.system) list_models() (in module macsypy.scripts.macsyfinder) list_package_vers() (macsypy.package.RemoteModelIndex method) list_packages() (macsypy.package.RemoteModelIndex method) LocalModelIndex (class in macsypy.package) loci_nb (macsypy.system.System property)

loci_num (macsypy.system.System property) log_level() (macsypy.config.Config method) Loner (class in macsypy.hit) loner (macsypy.cluster.Cluster property) (macsypy.gene.ModelGene property) (macsypy.hit.AbstractCounterpartHit property) (macsypy.hit.Loner property) (macsypy.hit.ModelHit property) LonerMultiSystem (class in macsypy.hit) loners_to_tsv() (in module macsypy.scripts.macsyfinder)

M

MacsydataError MacsyDataLimitError MacsyDefaults (class in macsypy.config) macsypy macsypy.database module macsypy.definition_parser module macsypy.error module macsypy.model_conf_parser module macsypy.scripts.macsyconfig module macsypy.scripts.macsydata module macsypy.scripts.macsyfinder module macsypy.scripts.macsyprofile module macsypy.search_genes module MacsypyError main() (in module macsypy.scripts.macsyconfig) (in module macsypy.scripts.macsydata) (in module macsypy.scripts.macsyfinder) (in module macsypy.scripts.macsyprofile) mandatory_hits (macsypy.system.AbstractUnordered property) match() (macsypy.system.OrderedMatchMaker method) (macsypy.system.UnorderedMatchMaker method) MatchMaker (class in macsypy.system) max (macsypy.database.RepliconInfo attribute) max_nb_genes (macsypy.model.Model property) max_nb_genes() (macsypy.config.Config method) merge() (macsypy.cluster.Cluster method) metadata (macsypy.package.Package property) MetaDefLoc (class in macsypy.registries) MetaSetOfHits (class in macsypy.system) min (macsypy.database.RepliconInfo attribute) min_genes_required (macsypy.model.Model property)

min_genes_required() (macsypy.config.Config method) min_mandatory_genes_required (macsypy.model.Model property) min_mandatory_genes_required() (macsypy.config.Config method) Model (class in macsypy.model) model (macsypy.gene.ModelGene property) Model family model_family_name (macsypy.gene.CoreGene property) ModelBank (class in macsypy.model) ModelConfParser (class in macsypy.model_conf_parser) ModelDefinition ModelGene (class in macsypy.gene) ModelHit (class in macsypy.hit) ModelInconsistencyError ModelLocation (class in macsypy.registries) ModelRegistry (class in macsypy.registries) models() (macsypy.registries.ModelRegistry method) models_dir() (macsypy.config.Config method) module macsypy.database macsypy.definition_parser macsypy.error macsypy.model_conf_parser macsypy.scripts.macsyconfig macsypy.scripts.macsydata macsypy.scripts.macsyfinder macsypy.scripts.macsyprofile macsypy.search_genes multi_loci (macsypy.model.Model property) (macsypy.system.System property) multi_loci() (macsypy.config.Config method) multi_model (macsypy.gene.ModelGene property) (macsypy.hit.ModelHit property) multi_system (macsypy.cluster.Cluster property) (macsypy.gene.ModelGene property) (macsypy.hit.AbstractCounterpartHit property) (macsypy.hit.ModelHit property) (macsypy.hit.MultiSystem property) MultiSystem (class in macsypy.hit) multisystems_to_tsv() (in module macsypy.scripts.macsyfinder)

N

name (macsypy.gene.CoreGene property) (macsypy.model.Model property)

neutral_hits (macsypy.system.AbstractUnordered property) NoneConfig (class in macsypy.config)

O

occurrence() (macsypy.system.System method) OptionError

OrderedHMMReport (class in macsypy.report) OrderedMatchMaker (class in macsypy.system) out_dir() (macsypy.config.Config method)

P

Package (class in macsypy.package) parse() (macsypy.definition_parser.DefinitionParser method) (macsypy.model_conf_parser.ModelConfParser method) (macsypy.scripts.macsyprofile.HmmProfile method) parse_args() (in module macsypy.scripts.macsyconfig) (in module macsypy.scripts.macsyfinder) (in module macsypy.scripts.macsyprofile) parse_filtering() (macsypy.model_conf_parser.ModelConfParser method)

parse_time() (in module macsypy.utils) parse_weights() (macsypy.model_conf_parser.ModelConfParser method) position (macsypy.system.AbstractSetOfHits property) present_genes() (macsypy.system.MatchMaker method) Profile (class in macsypy.profile) profile (macsypy.gene.CoreGene property) ProfileFactory (class in macsypy.profile) prolog() (in module macsypy.scripts.macsyconfig) pyproject.toml

R

README.md reasons (macsypy.system.UnlikelySystem property) rejected_candidates_to_tsv() (in module macsypy.scripts.macsyfinder) rejected_candidates_to_txt() (in module macsypy.scripts.macsyfinder) RejectedCandidate (class in macsypy.system) remote_exists() (macsypy.package.RemoteModelIndex method) RemoteModelIndex (class in macsypy.package)

replace() (macsypy.cluster.Cluster method) replicon_infos() (macsypy.database.RepliconDB method) replicon_name (macsypy.cluster.Cluster property) (macsypy.system.AbstractSetOfHits property) replicon_names() (macsypy.database.RepliconDB method) RepliconDB (class in macsypy.database) RepliconInfo (class in macsypy.database) root_name() (macsypy.registries.DefinitionLocation class method)

S

save() (macsypy.config.Config method) save_extract() (macsypy.report.HMMReport method) scan_models_dir() (in module macsypy.registries) score (macsypy.cluster.Cluster property) (macsypy.solution.Solution property) (macsypy.system.System property) search_genes() (in module macsypy.search_genes) search_systems() (in module macsypy.scripts.macsyfinder) serialize() (in module macsypy.scripts.macsyconfig) (macsypy.serialization.TsvLikelySystemSerializer method) (macsypy.serialization.TsvRejectedCandidatesSerializer method) (macsypy.serialization.TsvSolutionSerializer method) (macsypy.serialization.TsvSpecialHitSerializer method) (macsypy.serialization.TsvSystemSerializer method) (macsypy.serialization.TxtLikelySystemSerializer method) (macsypy.serialization.TxtSystemSerializer method) (macsypy.serialization.TxtUnikelySystemSerializer method) set_base_options() (in module macsypy.scripts.macsyconfig) set_general_options() (in module macsypy.scripts.macsyconfig) set_hmmer_options() (in module macsypy.scripts.macsyconfig) set_path_options() (in module macsypy.scripts.macsyconfig)

set_score_options() (in module macsypy.scripts.macsyconfig) set_section() (in module macsypy.scripts.macsyconfig) set_status() (macsypy.gene.ModelGene method) setup.cfg setup.py Solution (class in macsypy.solution) solutions_to_tsv() (in module macsypy.scripts.macsyfinder) sort_hits_by_status() (macsypy.system.MatchMaker method) sort_model_hits() (in module macsypy.hit) split_def_name() (in module macsypy.registries) split_fqn() (macsypy.registries.DefinitionLocation class method) status (macsypy.gene.Exchangeable property) (macsypy.gene.ModelGene property) summary_best_solution() (in module macsypy.scripts.macsyfinder) System (class in macsypy.system) SystemDetectionError systems (macsypy.solution.Solution property) systems_to_tsv() (in module macsypy.scripts.macsyfinder) systems_to_txt() (in module macsypy.scripts.macsyfinder) SystemSerializer (class in macsypy.serialization)

T

tests Theme (class in macsypy.scripts.macsyconfig) threads_available() (in module macsypy.utils) Timeout topology (macsypy.database.RepliconInfo attribute) TsvLikelySystemSerializer (class in macsypy.serialization)

TsvRejectedCandidatesSerializer (class in macsypy.serialization) TsvSolutionSerializer (class in macsypy.serialization) TsvSpecialHitSerializer (class in macsypy.serialization) TsvSystemSerializer (class in macsypy.serialization) TxtLikelySystemSerializer (class in macsypy.serialization) TxtSystemSerializer (class in macsypy.serialization) TxtUnikelySystemSerializer (class in macsypy.serialization)

U

unarchive_package() (macsypy.package.AbstractModelIndex method) unlikely_systems_to_txt() (in module macsypy.scripts.macsyfinder)

UnlikelySystem (class in macsypy.system) UnorderedMatchMaker (class in macsypy.system) utils

V

verbosity_to_log_level() (in module macsypy.scripts.macsydata) (in module macsypy.scripts.macsyprofile)

version (macsypy.registries.ModelLocation property)

W

wholeness (macsypy.system.AbstractSetOfHits property) worker_cpu() (in module macsypy.search_genes)

working_dir() (macsypy.config.Config method) write() (macsypy.scripts.macsyconfig.ConfigParserWithComments method)