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 attribute)

add_exchangeable() (macsypy.gene.Exchangeable method) (macsypy.gene.ModelGene method) add_new_gene() (macsypy.gene.GeneBank method) allowed_hits (macsypy.system.AbstractUnordered attribute) 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 attribute) CoreGene (class in macsypy.gene) CoreHit (class in macsypy.hit) count() (macsypy.system.AbstractSetOfHits method) counterpart (macsypy.hit.AbstractCounterpartHit attribute)

D

doc

E

EmptyFileError Exchangeable (class in macsypy.gene)

exchangeables (macsypy.gene.ModelGene attribute) 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 attribute)

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

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 attribute) hit_weights (macsypy.cluster.Cluster attribute) hit_weights() (macsypy.config.Config method) hits (macsypy.system.AbstractUnordered attribute) (macsypy.system.RejectedCandidate attribute) (macsypy.system.System attribute)

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.gene.ModelGene attribute) 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 attribute) (macsypy.gene.ModelGene attribute) 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 attribute) loci_num (macsypy.system.System attribute) log_level() (macsypy.config.Config method) Loner (class in macsypy.hit)

loner (macsypy.cluster.Cluster attribute) (macsypy.gene.ModelGene attribute) (macsypy.hit.AbstractCounterpartHit attribute) (macsypy.hit.Loner attribute) (macsypy.hit.ModelHit attribute) 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 attribute) 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 (macsypy.gene.ModelGene attribute) Model family model_family_name (macsypy.gene.CoreGene attribute) 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.system.System attribute) multi_loci() (macsypy.config.Config method) multi_model (macsypy.gene.ModelGene attribute) (macsypy.hit.ModelHit attribute) multi_system (macsypy.cluster.Cluster attribute) (macsypy.gene.ModelGene attribute) (macsypy.hit.AbstractCounterpartHit attribute) (macsypy.hit.ModelHit attribute) (macsypy.hit.MultiSystem attribute) MultiSystem (class in macsypy.hit)

N

name (macsypy.gene.CoreGene attribute)

neutral_hits (macsypy.system.AbstractUnordered attribute) 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 attribute)

present_genes() (macsypy.system.MatchMaker method) Profile (class in macsypy.profile) profile (macsypy.gene.CoreGene attribute) ProfileFactory (class in macsypy.profile) pyproject.toml

R

README.md reasons (macsypy.system.UnlikelySystem attribute) RejectedCandidate (class in macsypy.system) replace() (macsypy.cluster.Cluster method) replicon_infos() (macsypy.database.RepliconDB method)

replicon_name (macsypy.cluster.Cluster attribute) (macsypy.system.AbstractSetOfHits attribute) 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 attribute) (macsypy.system.System attribute) 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 attribute) (macsypy.gene.ModelGene attribute) 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 attribute)

working_dir() (macsypy.config.Config method)