Index

_

__call__() (macsypy.system.MetaSetOfHits method) __contains__() (macsypy.cluster.Cluster method) (macsypy.database.RepliconDB method) (macsypy.gene.GeneBank method) __eq__() (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) __getitem__() (macsypy.database.RepliconDB method) (macsypy.gene.GeneBank method) __gt__() (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) __hash__() (macsypy.gene.CoreGene method) (macsypy.gene.ModelGene method) (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) __init__() (macsypy.cluster.Cluster method) (macsypy.config.Config method) (macsypy.config.MacsyDefaults method) (macsypy.database.Indexes method) (macsypy.database.RepliconDB 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_conf_parser.ModelConfParser method) (macsypy.profile.Profile method) (macsypy.profile.ProfileFactory method) (macsypy.report.HMMReport 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) __len__() (macsypy.profile.Profile method) __lt__() (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) __str__() (macsypy.cluster.Cluster method) (macsypy.gene.ModelGene method) (macsypy.hit.AbstractCounterpartHit method) (macsypy.hit.CoreHit method) (macsypy.hit.ModelHit method) (macsypy.profile.Profile method) (macsypy.report.HMMReport method) (macsypy.system.LikelySystem method) (macsypy.system.RejectedCandidate method) (macsypy.system.System 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.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_conf_parser.ModelConfParser attribute) (macsypy.profile.Profile attribute) (macsypy.profile.ProfileFactory attribute) (macsypy.report.HMMReport attribute) (macsypy.serialization.SystemSerializer attribute) (macsypy.serialization.TsvRejectedCandidatesSerializer attribute) (macsypy.serialization.TsvSolutionSerializer attribute) (macsypy.serialization.TsvSpecialHitSerializer 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_replicon_consistency() (macsypy.cluster.Cluster method) _config_file_2_dict() (macsypy.config.Config method) _create_exchangeable_map() (macsypy.system.MatchMaker method) _fill_gembase_min_max() (macsypy.database.RepliconDB method) _fill_my_db() (macsypy.report.HMMReport method) _fill_ordered_min_max() (macsypy.database.RepliconDB method) _fill_topology() (macsypy.database.RepliconDB method) _get_model_conf_node() (macsypy.model_conf_parser.ModelConfParser 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) _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) _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) _str_2_tuple() (macsypy.config.Config method)

A

AbstractClusterizedHits (class in macsypy.system) AbstractCounterpartHit (class in macsypy.hit) AbstractSetOfHits (class in macsypy.system) AbstractUnordered (class in macsypy.system) accessory_hits() (macsypy.system.AbstractUnordered property)

add_exchangeable() (macsypy.gene.Exchangeable method) (macsypy.gene.ModelGene method) add_new_gene() (macsypy.gene.GeneBank 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

CITATION.yml Cluster (class in macsypy.cluster) compute_best_MSHit() (in module macsypy.hit) Config (class in macsypy.config) 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

doc

E

EmptyFileError Exchangeable (class in macsypy.gene)

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

F

fasta_iter() (in module macsypy.database) find_my_indexes() (macsypy.database.Indexes method) forbidden_hits() (macsypy.system.AbstractUnordered property)

fulfilled_function() (macsypy.cluster.Cluster method) (macsypy.system.AbstractClusterizedHits method) functions() (macsypy.cluster.Cluster property)

G

GembaseHMMReport (class in macsypy.report) GeneBank (class in macsypy.gene) GeneralHMMReport (class in macsypy.report) genes (macsypy.database.RepliconInfo attribute) genes_fqn() (macsypy.gene.GeneBank method) GeneStatus (class in macsypy.gene) get() (macsypy.database.RepliconDB method) get_best_hit_4_func() (in module macsypy.hit)

get_best_hits() (in module macsypy.hit) get_hits_encoding_multisystem() (macsypy.system.System method) get_loners() (macsypy.system.System method) get_multisystems() (macsypy.system.System method) get_position() (macsypy.hit.CoreHit method) get_profile() (macsypy.profile.ProfileFactory method) getter_maker() (macsypy.system.MetaSetOfHits method) guess_if_really_gembase() (macsypy.database.RepliconDB method)

H

hit() (macsypy.hit.ModelHit property) hit_weights() (macsypy.cluster.Cluster property) (macsypy.config.Config method) hits() (macsypy.system.AbstractUnordered property) (macsypy.system.RejectedCandidate 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) inter_gene_max_space() (macsypy.config.Config method) (macsypy.gene.ModelGene 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)

L

LikelySystem (class in macsypy.system) 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)

M

MacsydataError MacsyDataLimitError MacsyDefaults (class in macsypy.config) macsypy macsypy.database (module) macsypy.error (module) macsypy.model_conf_parser (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) merge() (macsypy.cluster.Cluster method) MetaSetOfHits (class in macsypy.system) min (macsypy.database.RepliconInfo attribute) min_genes_required() (macsypy.config.Config method) min_mandatory_genes_required() (macsypy.config.Config method)

Model Model family model() (macsypy.gene.ModelGene property) model_family_name() (macsypy.gene.CoreGene property) ModelConfParser (class in macsypy.model_conf_parser) ModelDefinition ModelGene (class in macsypy.gene) ModelHit (class in macsypy.hit) ModelInconsistencyError models_dir() (macsypy.config.Config method) multi_loci() (macsypy.config.Config method) (macsypy.system.System property) 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)

N

name() (macsypy.gene.CoreGene 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

parse() (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) pyproject.toml

R

README.md reasons() (macsypy.system.UnlikelySystem property) RejectedCandidate (class in macsypy.system) 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)

S

save() (macsypy.config.Config method) save_extract() (macsypy.report.HMMReport method) score() (macsypy.cluster.Cluster property) (macsypy.system.System property) serialize() (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_status() (macsypy.gene.ModelGene method) setup.cfg setup.py Solution sort_hits_by_status() (macsypy.system.MatchMaker method) sort_model_hits() (in module macsypy.hit) status() (macsypy.gene.Exchangeable property) (macsypy.gene.ModelGene property) System (class in macsypy.system) SystemDetectionError SystemSerializer (class in macsypy.serialization)

T

tests 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

UnlikelySystem (class in macsypy.system)

UnorderedMatchMaker (class in macsypy.system) utils

W

wholeness() (macsypy.system.AbstractSetOfHits property)

working_dir() (macsypy.config.Config method)