Index

_

__call__() (macsypy.system.MetaSetOfHits method) __contains__() (macsypy.cluster.Cluster method) (macsypy.database.RepliconDB method) (macsypy.gene.GeneBank method) (macsypy.model.ModelBank method) __eq__() (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) (macsypy.registries.ModelLocation 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.gene.CoreGene method) (macsypy.gene.ModelGene method) (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) (macsypy.model.Model method) (macsypy.registries.DefinitionLocation method) __init__() (macsypy.cluster.Cluster method) (macsypy.config.Config method), [1] (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.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.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.RejectedClusters 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) __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.system.LikelySystem method) (macsypy.system.RejectedClusters method) (macsypy.system.UnlikelySystem method)

__weakref__ (macsypy.cluster.Cluster attribute) (macsypy.config.Config attribute), [1] (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.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.serialization.SystemSerializer attribute) (macsypy.serialization.TsvSolutionSerializer attribute) (macsypy.solution.Solution attribute) (macsypy.system.AbstractSetOfHits attribute) (macsypy.system.HitSystemTracker attribute) (macsypy.system.MatchMaker attribute) _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), [1] _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) _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) _scan_definitions() (macsypy.registries.ModelLocation method) _scan_profiles() (macsypy.registries.ModelLocation method) _set_command_line_config() (macsypy.config.Config method), [1] _set_db_type() (macsypy.config.Config method), [1] _set_default_config() (macsypy.config.Config method), [1] _set_inter_gene_max_space() (macsypy.config.Config method), [1] _set_max_nb_genes() (macsypy.config.Config method), [1] _set_min_genes_required() (macsypy.config.Config method), [1] _set_min_mandatory_genes_required() (macsypy.config.Config method), [1] _set_model_config() (macsypy.config.Config method), [1] _set_models() (macsypy.config.Config method), [1] _set_models_dir() (macsypy.config.Config method), [1] _set_multi_loci() (macsypy.config.Config method), [1] _set_options() (macsypy.config.Config method), [1] _set_previous_run_config() (macsypy.config.Config method), [1] _set_project_config_file() (macsypy.config.Config method), [1] _set_replicon_topology() (macsypy.config.Config method), [1] _set_sequence_db() (macsypy.config.Config method), [1] _set_system_models_dir() (macsypy.config.Config method), [1] _set_system_wide_config() (macsypy.config.Config method), [1] _set_topology_file() (macsypy.config.Config method), [1] _set_user_config_file() (macsypy.config.Config method), [1] _set_user_wide_config() (macsypy.config.Config method), [1] _sorted_systems() (macsypy.solution.Solution method) _str_2_tuple() (macsypy.config.Config method), [1] _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_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) average_wholeness() (macsypy.solution.Solution property)

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) combine_clusters() (in module macsypy.solution) combine_multisystems() (in module macsypy.solution) compute_best_MSHit() (in module macsypy.hit)

Config (class in macsypy.config), [1] CONTRIBUTING CONTRIBUTORS COPYING COPYRIGHT 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)

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) 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_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_profiles_names() (macsypy.registries.ModelLocation method) get_replicon_names() (in module macsypy.utils) getter_maker() (macsypy.system.MetaSetOfHits method)

H

help() (macsypy.package.Package method) hit() (macsypy.hit.ModelHit property) hit_weights() (macsypy.config.Config method), [1] hits() (macsypy.system.AbstractUnordered property) (macsypy.system.RejectedClusters 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), [1] HMMReport (class in macsypy.report)

I

Indexes (class in macsypy.database) info() (macsypy.package.Package method) inter_gene_max_space() (macsypy.config.Config method), [1] (macsypy.gene.ModelGene property) (macsypy.model.Model property) 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), [1]

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)

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.search_genes 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.config.Config method), [1] (macsypy.model.Model property) 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.config.Config method), [1] (macsypy.model.Model property) min_mandatory_genes_required() (macsypy.config.Config method), [1] (macsypy.model.Model property)

Model (class in macsypy.model) Model family model() (macsypy.gene.ModelGene property) 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), [1] module macsypy.database macsypy.definition_parser macsypy.error macsypy.model_conf_parser macsypy.search_genes multi_loci() (macsypy.config.Config method), [1] (macsypy.model.Model property) (macsypy.system.System 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)

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), [1]

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) replace() (macsypy.cluster.Cluster method)

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), [1] save_extract() (macsypy.report.HMMReport method) scan_models_dir() (in module macsypy.registries) score() (macsypy.solution.Solution property) (macsypy.system.System property) search_genes() (in module macsypy.search_genes) serialize() (macsypy.serialization.TsvLikelySystemSerializer 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_status() (macsypy.gene.ModelGene method) setup.py Solution (class in macsypy.solution) sort_hits_by_status() (macsypy.system.MatchMaker method) sort_model_hits() (in module macsypy.hit) split_def_name() (in module macsypy.registries) status() (macsypy.gene.Exchangeable property) (macsypy.gene.ModelGene property) System (class in macsypy.system) SystemDetectionError systems() (macsypy.solution.Solution property) SystemSerializer (class in macsypy.serialization)

T

tests topology (macsypy.database.RepliconInfo attribute) TsvLikelySystemSerializer (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) UnlikelySystem (class in macsypy.system)

UnorderedMatchMaker (class in macsypy.system) utils

W

wholeness() (macsypy.system.AbstractSetOfHits property)

working_dir() (macsypy.config.Config method), [1]