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) __eq__() (macsypy.hit.Hit method) (macsypy.hit.HitWeight method) (macsypy.hit.ValidHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation method) __getitem__() (macsypy.database.RepliconDB method) (macsypy.gene.GeneBank method) (macsypy.model.ModelBank method) (macsypy.registries.ModelRegistry method) __getnewargs__() (macsypy.database.RepliconInfo method) __gt__() (macsypy.hit.Hit method) (macsypy.hit.ValidHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation method) __hash__ (macsypy.hit.ValidHit attribute) (macsypy.registries.ModelLocation attribute) __hash__() (macsypy.gene.CoreGene method) (macsypy.gene.ModelGene method) (macsypy.hit.Hit method) (macsypy.hit.HitWeight method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation 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.Hit method) (macsypy.hit.HitWeight method) (macsypy.hit.ValidHit 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.serialization.TsvSolutionSerializer method) (macsypy.system.AbstractSetOfHits method) (macsypy.system.AbstractUnordered method) (macsypy.system.ClusterSystemTracker method) (macsypy.system.HitSystemTracker method) (macsypy.system.MatchMaker method) (macsypy.system.OrderedMatchMaker method) (macsypy.system.RejectedClusters method) (macsypy.system.System method) (macsypy.system.UnlikelySystem method) __iter__() (macsypy.database.Indexes method) (macsypy.gene.GeneBank method) (macsypy.model.ModelBank method) __len__() (macsypy.model.ModelBank method) (macsypy.profile.Profile method) __lt__() (macsypy.hit.Hit method) (macsypy.hit.ValidHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation method) __new__() (macsypy.database.RepliconInfo static method) (macsypy.package.AbstractModelIndex static method) __repr__() (macsypy.database.RepliconInfo method) (macsypy.hit.HitWeight method) __setattr__() (macsypy.hit.HitWeight method) __str__() (macsypy.cluster.Cluster method) (macsypy.gene.ModelGene method) (macsypy.hit.Hit 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.system.LikelySystem method) (macsypy.system.RejectedClusters method) (macsypy.system.UnlikelySystem method)

__weakref__ (macsypy.cluster.Cluster attribute) (macsypy.config.Config attribute) (macsypy.config.MacsyDefaults 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.Hit attribute) (macsypy.hit.HitWeight attribute) (macsypy.hit.ValidHit 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.serialization.SystemSerializer attribute) (macsypy.serialization.TsvSolutionSerializer attribute) (macsypy.system.AbstractSetOfHits attribute) (macsypy.system.ClusterSystemTracker attribute) (macsypy.system.HitSystemTracker attribute) (macsypy.system.MatchMaker attribute) _asdict() (macsypy.database.RepliconInfo method) _build_my_db() (macsypy.report.HMMReport 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) _fill_ordered_min_max() (macsypy.database.RepliconDB method) _fill_topology() (macsypy.database.RepliconDB method) _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) _index_dir() (macsypy.database.Indexes method) _load_metadata() (macsypy.package.Package method) _make() (macsypy.database.RepliconInfo class method) _parse_exchangeable() (macsypy.definition_parser.DefinitionParser method) _parse_genes() (macsypy.definition_parser.DefinitionParser method) _parse_hmm_body() (macsypy.report.HMMReport method) _parse_hmm_header() (macsypy.report.HMMReport method) _parse_section() (macsypy.model_conf_parser.ModelConfParser method) _profile_features() (macsypy.profile.Profile method) _replace() (macsypy.database.RepliconInfo method) _scan_definitions() (macsypy.registries.ModelLocation method) _scan_profiles() (macsypy.registries.ModelLocation method) _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_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_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) _str_2_tuple() (macsypy.config.Config method) _url_json() (macsypy.package.RemoteModelIndex method)

A

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_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) allowed_hits (macsypy.system.AbstractUnordered property) alternate_of() (macsypy.gene.Exchangeable method) (macsypy.gene.ModelGene method)

B

best_hit() (macsypy.report.HMMReport method)

build() (macsypy.database.Indexes method) build_clusters() (in module macsypy.cluster)

C

check() (macsypy.package.Package method) check_consistency() (macsypy.definition_parser.DefinitionParser method) CITATION.yml Cluster (class in macsypy.cluster) ClusterSystemTracker (class in macsypy.system)

Config (class in macsypy.config) CONTRIBUTING CONTRIBUTORS COPYING COPYRIGHT CoreGene (class in macsypy.gene) count() (macsypy.system.AbstractSetOfHits method)

D

DefinitionLocation (class in macsypy.registries) DefinitionParser (class in macsypy.definition_parser)

doc download() (macsypy.package.RemoteModelIndex method)

E

etc 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) fasta_iter() (in module macsypy.database) filter() (macsypy.model.Model method) filter_loners() (in module macsypy.cluster)

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)

G

GembaseHMMReport (class in macsypy.report) GeneBank (class in macsypy.gene) GeneralHMMReport (class in macsypy.report) genes (macsypy.database.RepliconInfo attribute) (macsypy.model.Model property) 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_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_loners() (in module macsypy.cluster) get_metadata() (macsypy.package.RemoteModelIndex method) get_position() (macsypy.hit.Hit method) get_profile() (macsypy.profile.ProfileFactory method) (macsypy.registries.ModelLocation method) get_profiles_names() (macsypy.registries.ModelLocation method) getter_maker() (macsypy.system.MetaSetOfHits method)

H

help() (macsypy.package.Package method) Hit (class in macsypy.hit) hit_weights() (macsypy.config.Config method) hits (macsypy.system.AbstractUnordered property) (macsypy.system.RejectedClusters property) (macsypy.system.System property)

HitSystemTracker (class in macsypy.system) HitWeight (class in macsypy.hit) hmmer_dir() (macsypy.config.Config method) HMMReport (class in macsypy.report)

I

Indexes (class in macsypy.database) info() (macsypy.package.Package method) 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

LikelySystem (class in macsypy.system) 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 (macsypy.cluster.Cluster property) (macsypy.gene.ModelGene property) (macsypy.hit.ValidHit property)

M

MacsydataError MacsyDataLimitError MacsyDefaults (class in macsypy.config) macsypy macsypy.cluster module macsypy.config module macsypy.database module macsypy.definition_parser module macsypy.error module macsypy.hit module macsypy.model_conf_parser module macsypy.package module macsypy.registries module macsypy.search_genes module macsypy.serialization module macsypy.solution module macsypy.system module macsypy.utils module MacsypyError 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) 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) ModelInconsistencyError ModelLocation (class in macsypy.registries) ModelRegistry (class in macsypy.registries) models() (macsypy.registries.ModelRegistry method) models_dir() (macsypy.config.Config method) module macsypy.cluster macsypy.config macsypy.database macsypy.definition_parser macsypy.error macsypy.hit macsypy.model_conf_parser macsypy.package macsypy.registries macsypy.search_genes macsypy.serialization macsypy.solution macsypy.system macsypy.utils multi_loci (macsypy.model.Model property) (macsypy.system.System property) multi_loci() (macsypy.config.Config method) multi_system (macsypy.gene.ModelGene property) (macsypy.hit.ValidHit property)

N

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

neutral_hits (macsypy.system.AbstractUnordered property)

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) parse_filtering() (macsypy.model_conf_parser.ModelConfParser method) 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)

R

README.md reasons (macsypy.system.UnlikelySystem property) RejectedClusters (class in macsypy.system) remote_exists() (macsypy.package.RemoteModelIndex method) RemoteModelIndex (class in macsypy.package) replicon_infos() (macsypy.database.RepliconDB method)

replicon_name (macsypy.system.AbstractSetOfHits property) replicon_names() (macsypy.database.RepliconDB method) RepliconDB (class in macsypy.database) RepliconInfo (class in macsypy.database) requirements.txt requirements_dev.txt

S

save() (macsypy.config.Config method) save_extract() (macsypy.report.HMMReport method) scan_models_dir() (in module macsypy.registries) score (macsypy.system.System property) search_genes() (in module macsypy.search_genes) serialize() (macsypy.serialization.TsvSolutionSerializer method) (macsypy.serialization.TsvSystemSerializer method) (macsypy.serialization.TxtSystemSerializer method)

setup.py Solution sort_hits_by_status() (macsypy.system.MatchMaker method) split_def_name() (in module macsypy.registries) System (class in macsypy.system) SystemDetectionError SystemSerializer (class in macsypy.serialization)

T

tests topology (macsypy.database.RepliconInfo attribute)

TsvSolutionSerializer (class in macsypy.serialization) TsvSystemSerializer (class in macsypy.serialization) TxtSystemSerializer (class in macsypy.serialization)

U

unarchive_package() (macsypy.package.AbstractModelIndex method) UnlikelySystem (class in macsypy.system)

UnorderedMatchMaker (class in macsypy.system) utils

V

ValidHit (class in macsypy.hit)

W

wholeness (macsypy.system.AbstractSetOfHits property)

working_dir() (macsypy.config.Config method)