Index

_

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

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

A

AbstractClusterizedHits (class in macsylib.system) AbstractCounterpartHit (class in macsylib.hit) AbstractModelIndex (class in macsylib.model_package) AbstractSetOfHits (class in macsylib.system) AbstractUnordered (class in macsylib.system) accessory_hits (macsylib.system.AbstractUnordered property) add() (macsylib.registries.ModelRegistry method) add_exchangeable() (macsylib.gene.Exchangeable method) (macsylib.gene.ModelGene method)

add_model() (macsylib.model.ModelBank method) add_new_gene() (macsylib.gene.GeneBank method) add_subdefinition() (macsylib.registries.DefinitionLocation method) all() (macsylib.registries.DefinitionLocation method) allowed_hits (macsylib.system.AbstractUnordered property) alternate_of() (macsylib.gene.Exchangeable method) (macsylib.gene.ModelGene method) average_wholeness (macsylib.solution.Solution property)

B

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

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

C

check() (macsylib.model_package.ModelPackage method) check_consistency() (macsylib.definition_parser.DefinitionParser method) closest_hit() (in module macsylib.cluster) Cluster (class in macsylib.cluster), [1] clusterize_hits_around_key_genes() (in module macsylib.cluster) clusterize_hits_on_distance_only() (in module macsylib.cluster) cmd_name() (in module macsylib.scripts.macsydata) codemeta.json combine_clusters() (in module macsylib.solution) combine_multisystems() (in module macsylib.solution)

compute_best_MSHit() (in module macsylib.hit) Config (class in macsylib.config) CONTRIBUTING CONTRIBUTORS COPYING COPYRIGHT core_gene (macsylib.gene.ModelGene property) CoreGene (class in macsylib.gene) CoreHit (class in macsylib.hit) count() (macsylib.system.AbstractSetOfHits method) counterpart (macsylib.hit.AbstractCounterpartHit property)

D

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

do_init_package() (in module macsylib.scripts.macsydata) do_install() (in module macsylib.scripts.macsydata) do_list() (in module macsylib.scripts.macsydata) do_search() (in module macsylib.scripts.macsydata) do_show_definition() (in module macsylib.scripts.macsydata) do_show_package() (in module macsylib.scripts.macsydata) do_uninstall() (in module macsylib.scripts.macsydata) doc download() (macsylib.model_package.RemoteModelIndex method)

E

EmptyFileError Exchangeable (class in macsylib.gene)

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

F

family_name (macsylib.model.Model property) (macsylib.registries.DefinitionLocation property) fasta_iter() (in module macsylib.database) filter() (macsylib.model.Model method) find_best_solutions() (in module macsylib.solution)

find_my_indexes() (macsylib.database.Indexes method) forbidden_hits (macsylib.system.AbstractUnordered property) fulfilled_function() (macsylib.cluster.Cluster method), [1] (macsylib.system.AbstractClusterizedHits method) functions (macsylib.cluster.Cluster property), [1]

G

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

get_gene() (macsylib.model.Model method) get_gene_name() (in module macsylib.scripts.macsyprofile) get_hits_encoding_multisystem() (macsylib.system.System method) get_loners() (macsylib.system.System method) get_metadata() (macsylib.model_package.RemoteModelIndex method) get_multisystems() (macsylib.system.System method) get_profile() (macsylib.profile.ProfileFactory method) (macsylib.registries.ModelLocation method) get_profile_len() (in module macsylib.scripts.macsyprofile) get_profiles_names() (macsylib.registries.ModelLocation method) get_replicon_names() (in module macsylib.utils) get_version_message() (in module macsylib.scripts.macsyprofile) getter_maker() (macsylib.system.MetaSetOfHits method) guess_if_really_gembase() (macsylib.database.RepliconDB method)

H

help() (macsylib.model_package.ModelPackage method) hit (macsylib.hit.ModelHit property) hit_weights (macsylib.cluster.Cluster property), [1] hit_weights() (macsylib.config.Config method) hits (macsylib.cluster.Cluster property), [1] (macsylib.system.AbstractUnordered property) (macsylib.system.RejectedCandidate property) (macsylib.system.System property)

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

I

Indexes (class in macsylib.database) info() (macsylib.model_package.ModelPackage method) init_logger() (in module macsylib.scripts.macsydata) (in module macsylib.scripts.macsyprofile) inter_gene_max_space (macsylib.gene.ModelGene property) (macsylib.model.Model property) inter_gene_max_space() (macsylib.config.Config method) is_a() (in module macsylib.cluster)

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

J

join_def_path() (in module macsylib.registries)

L

LightHit (class in macsylib.scripts.macsyprofile) LikelySystem (class in macsylib.system) list_package_vers() (macsylib.model_package.RemoteModelIndex method) list_packages() (macsylib.model_package.RemoteModelIndex method) LocalModelIndex (class in macsylib.model_package) loci_nb (macsylib.system.System property) loci_num (macsylib.system.System property)

log_level() (macsylib.config.Config method) Loner (class in macsylib.hit) loner (macsylib.cluster.Cluster property), [1] (macsylib.gene.ModelGene property) (macsylib.hit.AbstractCounterpartHit property) (macsylib.hit.Loner property) (macsylib.hit.ModelHit property) LonerMultiSystem (class in macsylib.hit)

M

MacsydataError MacsyDataLimitError MacsyDefaults (class in macsylib.config) macsylib macsylib.cluster module macsylib.database module macsylib.definition_parser module macsylib.error module macsylib.model_conf_parser module macsylib.scripts.macsydata module macsylib.scripts.macsyprofile module macsylib.search_genes module MacsylibError main() (in module macsylib.scripts.macsydata) (in module macsylib.scripts.macsyprofile) mandatory_hits (macsylib.system.AbstractUnordered property) match() (macsylib.system.OrderedMatchMaker method) (macsylib.system.UnorderedMatchMaker method) MatchMaker (class in macsylib.system) max (macsylib.database.RepliconInfo attribute) max_nb_genes (macsylib.model.Model property) max_nb_genes() (macsylib.config.Config method) merge() (macsylib.cluster.Cluster method), [1] metadata (macsylib.model_package.ModelPackage property) MetaDefLoc (class in macsylib.registries) MetaSetOfHits (class in macsylib.system) min (macsylib.database.RepliconInfo attribute) min_genes_required (macsylib.model.Model property) min_genes_required() (macsylib.config.Config method)

min_mandatory_genes_required (macsylib.model.Model property) min_mandatory_genes_required() (macsylib.config.Config method) Model (class in macsylib.model) model (macsylib.gene.ModelGene property) Model family model_family_name (macsylib.gene.CoreGene property) ModelBank (class in macsylib.model) ModelConfParser (class in macsylib.model_conf_parser) ModelDefinition ModelGene (class in macsylib.gene) ModelHit (class in macsylib.hit) ModelInconsistencyError ModelLocation (class in macsylib.registries) ModelPackage (class in macsylib.model_package) ModelRegistry (class in macsylib.registries) models() (macsylib.registries.ModelRegistry method) models_dir() (macsylib.config.Config method) module macsylib.cluster macsylib.database macsylib.definition_parser macsylib.error macsylib.model_conf_parser macsylib.scripts.macsydata macsylib.scripts.macsyprofile macsylib.search_genes multi_loci (macsylib.model.Model property) (macsylib.system.System property) multi_loci() (macsylib.config.Config method) multi_model (macsylib.gene.ModelGene property) (macsylib.hit.ModelHit property) multi_system (macsylib.cluster.Cluster property), [1] (macsylib.gene.ModelGene property) (macsylib.hit.AbstractCounterpartHit property) (macsylib.hit.ModelHit property) (macsylib.hit.MultiSystem property) MultiSystem (class in macsylib.hit)

N

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

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

O

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

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

P

parse() (macsylib.definition_parser.DefinitionParser method) (macsylib.model_conf_parser.ModelConfParser method) (macsylib.scripts.macsyprofile.HmmProfile method) parse_args() (in module macsylib.scripts.macsyprofile) parse_filtering() (macsylib.model_conf_parser.ModelConfParser method) parse_time() (in module macsylib.utils)

parse_weights() (macsylib.model_conf_parser.ModelConfParser method) position (macsylib.system.AbstractSetOfHits property) present_genes() (macsylib.system.MatchMaker method) Profile (class in macsylib.profile) profile (macsylib.gene.CoreGene property) ProfileFactory (class in macsylib.profile) pyproject.toml

R

README.md reasons (macsylib.system.RejectedCandidate property) (macsylib.system.UnlikelySystem property) RejectedCandidate (class in macsylib.system) remote_exists() (macsylib.model_package.RemoteModelIndex method) RemoteModelIndex (class in macsylib.model_package) replace() (macsylib.cluster.Cluster method), [1]

replicon_infos() (macsylib.database.RepliconDB method) replicon_name (macsylib.cluster.Cluster property), [1] (macsylib.system.AbstractSetOfHits property) replicon_names() (macsylib.database.RepliconDB method) RepliconDB (class in macsylib.database) RepliconInfo (class in macsylib.database) result_header() (in module macsylib.scripts.macsyprofile) root_name() (macsylib.registries.DefinitionLocation class method)

S

save() (macsylib.config.Config method) save_extract() (macsylib.report.HMMReport method) scaffold_to_cluster() (in module macsylib.cluster) scan_models_dir() (in module macsylib.registries) score (macsylib.cluster.Cluster property), [1] (macsylib.solution.Solution property) (macsylib.system.System property) search_genes() (in module macsylib.search_genes) serialize() (macsylib.serialization.TsvLikelySystemSerializer method) (macsylib.serialization.TsvRejectedCandidatesSerializer method) (macsylib.serialization.TsvSolutionSerializer method) (macsylib.serialization.TsvSpecialHitSerializer method) (macsylib.serialization.TsvSystemSerializer method) (macsylib.serialization.TxtLikelySystemSerializer method) (macsylib.serialization.TxtSystemSerializer method) (macsylib.serialization.TxtUnikelySystemSerializer method)

set_status() (macsylib.gene.ModelGene method) setup.py Solution (class in macsylib.solution) sort_hits_by_status() (macsylib.system.MatchMaker method) sort_model_hits() (in module macsylib.hit) split_cluster_on_key_genes() (in module macsylib.cluster) split_def_name() (in module macsylib.registries) split_fqn() (macsylib.registries.DefinitionLocation class method) status (macsylib.gene.Exchangeable property) (macsylib.gene.ModelGene property) System (class in macsylib.system) SystemDetectionError systems (macsylib.solution.Solution property) SystemSerializer (class in macsylib.serialization)

T

tests threads_available() (in module macsylib.utils) Timeout topology (macsylib.database.RepliconInfo attribute) TsvLikelySystemSerializer (class in macsylib.serialization) TsvRejectedCandidatesSerializer (class in macsylib.serialization)

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

U

unarchive_package() (macsylib.model_package.AbstractModelIndex method)

UnlikelySystem (class in macsylib.system) UnorderedMatchMaker (class in macsylib.system)

V

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

version (macsylib.registries.ModelLocation property)

W

wholeness (macsylib.system.AbstractSetOfHits property)

worker_cpu() (in module macsylib.search_genes) working_dir() (macsylib.config.Config method)