Index

_

__cmp__() (macsypy.report.Hit method) __contains__() (macsypy.database.RepliconDB method) (macsypy.gene.GeneBank method) (macsypy.system.SystemBank method) __eq__() (macsypy.gene.Gene method) (macsypy.report.Hit method) __getitem__() (macsypy.database.RepliconDB method) (macsypy.gene.GeneBank method) (macsypy.system.SystemBank method) __getnewargs__() (macsypy.database.RepliconInfo method) __getstate__() (macsypy.database.RepliconInfo method) __init__() (macsypy.config.Config method) (macsypy.database.Indexes method) (macsypy.database.RepliconDB method) (macsypy.gene.Analog method) (macsypy.gene.Gene method) (macsypy.gene.Homolog method) (macsypy.gene.Profile method) (macsypy.report.HMMReport method) (macsypy.report.Hit method) (macsypy.search_systems.Cluster method) (macsypy.search_systems.ClustersHandler method) (macsypy.search_systems.SystemOccurence method) (macsypy.search_systems.systemDetectionReportOrdered method) (macsypy.search_systems.systemDetectionReportUnordered method) (macsypy.search_systems.validSystemHit method) (macsypy.system.System method) (macsypy.system_parser.SystemParser method) __iter__() (macsypy.gene.GeneBank method) (macsypy.system.SystemBank method) __len__() (macsypy.gene.Profile method) (macsypy.search_systems.Cluster method) (macsypy.system.SystemBank method) __metaclass__ (macsypy.report.HMMReport attribute) __new__() (macsypy.database.RepliconInfo static method) __repr__() (macsypy.database.RepliconInfo method) __str__() (macsypy.gene.Gene method) (macsypy.gene.Profile method) (macsypy.report.HMMReport method) (macsypy.report.Hit method) (macsypy.search_systems.Cluster method) (macsypy.search_systems.SystemOccurence method) __weakref__ (macsypy.config.Config attribute) (macsypy.database.Indexes attribute) (macsypy.database.RepliconDB attribute) (macsypy.gene.Analog attribute) (macsypy.gene.Gene attribute) (macsypy.gene.GeneBank attribute) (macsypy.gene.Homolog attribute) (macsypy.gene.Profile attribute) (macsypy.macsypy_error.MacsypyError attribute) (macsypy.report.HMMReport attribute) (macsypy.report.Hit attribute) (macsypy.search_systems.Cluster attribute) (macsypy.search_systems.ClustersHandler attribute) (macsypy.search_systems.SystemNameGenerator attribute) (macsypy.search_systems.SystemOccurence attribute) (macsypy.search_systems.validSystemHit attribute) (macsypy.system.System attribute) (macsypy.system.SystemBank attribute) (macsypy.system_parser.SystemParser attribute) _asdict() (macsypy.database.RepliconInfo method) _build_hmmer_indexes() (macsypy.database.Indexes method) _build_my_db() (macsypy.report.HMMReport method) _build_my_indexes() (macsypy.database.Indexes method)

_computeBasename() (macsypy.search_systems.SystemNameGenerator method) _create_genes() (macsypy.system_parser.SystemParser method) _create_system() (macsypy.system_parser.SystemParser method) _fill() (macsypy.system_parser.SystemParser 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) _hit_start() (macsypy.report.HMMReport method) _len() (macsypy.gene.Profile method) _make() (macsypy.database.RepliconInfo class method) _match2json() (macsypy.search_systems.systemDetectionReportOrdered method) _parse_analog() (macsypy.system_parser.SystemParser method) _parse_hmm_body() (macsypy.report.HMMReport method) _parse_hmm_header() (macsypy.report.HMMReport method) _parse_homolog() (macsypy.system_parser.SystemParser method) _replace() (macsypy.database.RepliconInfo method) _validate() (macsypy.config.Config method)

A

accessory_genes (macsypy.system.System attribute) add() (macsypy.search_systems.Cluster method) add_accessory_gene() (macsypy.system.System method) add_analog() (macsypy.gene.Gene method) add_forbidden_gene() (macsypy.system.System method) add_gene() (macsypy.gene.GeneBank method)

add_homolog() (macsypy.gene.Gene method) add_mandatory_gene() (macsypy.system.System method) add_system() (macsypy.system.SystemBank method) Analog (class in macsypy.gene) analyze_clusters_replicon() (in module macsypy.search_systems)

B

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

build_clusters() (in module macsypy.search_systems) build_indexes (macsypy.config.Config attribute)

C

check_consistency() (macsypy.system_parser.SystemParser method) circularize() (macsypy.search_systems.ClustersHandler method) Cluster (class in macsypy.search_systems) ClustersHandler (class in macsypy.search_systems) compatible_systems (macsypy.search_systems.Cluster attribute) compute_missing_genes_list() (macsypy.search_systems.SystemOccurence method) compute_system_length() (macsypy.search_systems.SystemOccurence method)

Config (class in macsypy.config) count_genes() (macsypy.search_systems.SystemOccurence method) count_genes_tot() (macsypy.search_systems.SystemOccurence method) count_missing_genes() (macsypy.search_systems.SystemOccurence method) counter_output() (macsypy.search_systems.systemDetectionReportOrdered method) coverage_profile (macsypy.config.Config attribute)

D

db_type (macsypy.config.Config attribute) decision_rule() (macsypy.search_systems.SystemOccurence method)

def_dir (macsypy.config.Config attribute) disambiguate_cluster() (in module macsypy.search_systems)

E

e_value_res (macsypy.config.Config attribute) exchangeable (macsypy.gene.Gene attribute)

execute() (macsypy.gene.Profile method) extract() (macsypy.report.GembaseHMMReport method) (macsypy.report.GeneralHMMReport method) (macsypy.report.HMMReport method) (macsypy.report.OrderedHMMReport method)

F

fasta_iter() (in module macsypy.database) fill_with_cluster() (macsypy.search_systems.SystemOccurence method) fill_with_hits() (macsypy.search_systems.SystemOccurence method) fill_with_multi_systems_genes() (macsypy.search_systems.SystemOccurence method)

find_hmmer_indexes() (macsypy.database.Indexes method) find_my_indexes() (macsypy.database.Indexes method) forbidden_genes (macsypy.system.System attribute)

G

GembaseHMMReport (class in macsypy.report) Gene (class in macsypy.gene) gene (macsypy.gene.Analog attribute) (macsypy.gene.Homolog attribute) gene_ref (macsypy.gene.Analog attribute) (macsypy.gene.Homolog attribute) GeneBank (class in macsypy.gene) GeneralHMMReport (class in macsypy.report) genes (macsypy.database.RepliconInfo attribute) get() (macsypy.database.RepliconDB method) get_analogs() (macsypy.gene.Gene method) get_best_hits() (in module macsypy.search_systems) get_compatible_systems() (in module macsypy.search_systems) (macsypy.gene.Gene method) get_gene() (macsypy.system.System method)

get_gene_counter_output() (macsypy.search_systems.SystemOccurence method) get_gene_ref() (macsypy.search_systems.SystemOccurence method) (macsypy.system.System method) get_homologs() (macsypy.gene.Gene method) get_position() (macsypy.report.Hit method) get_profile() (macsypy.gene.ProfileFactory method) get_summary() (macsypy.search_systems.SystemOccurence method) get_summary_header() (macsypy.search_systems.SystemOccurence method) get_summary_unordered() (macsypy.search_systems.SystemOccurence method) get_syst_inter_gene_max_space() (macsypy.report.Hit method) get_system_name_unordered() (macsypy.search_systems.SystemOccurence method) get_system_unique_name() (macsypy.search_systems.SystemOccurence method) getSystemName() (macsypy.search_systems.SystemNameGenerator method)

H

Hit (class in macsypy.report) hmmer_dir (macsypy.config.Config attribute) hmmer_exe (macsypy.config.Config attribute)

HMMReport (class in macsypy.report) Homolog (class in macsypy.gene)

I

i_evalue_sel (macsypy.config.Config attribute) index_db_exe (macsypy.config.Config attribute) Indexes (class in macsypy.database) inter_gene_max_space (macsypy.gene.Gene attribute) (macsypy.system.System attribute) inter_gene_max_space() (macsypy.config.Config method) is_accessory() (macsypy.gene.Gene method) is_aligned() (macsypy.gene.Homolog method) is_analog() (macsypy.gene.Gene method)

is_authorized() (macsypy.gene.Gene method) is_complete() (macsypy.search_systems.SystemOccurence method) is_forbidden() (macsypy.gene.Gene method) is_homolog() (macsypy.gene.Gene method) is_mandatory() (macsypy.gene.Gene method) items() (macsypy.database.RepliconDB method) iteritems() (macsypy.database.RepliconDB method)

J

json_output() (macsypy.search_systems.systemDetectionReportOrdered method) (macsypy.search_systems.systemDetectionReportUnordered method)

L

loner (macsypy.gene.Gene attribute)

M

macsypy.config (module) macsypy.database (module) macsypy.gene (module), [1], [2], [3], [4], [5] macsypy.macsypy_error (module) macsypy.report (module), [1], [2], [3], [4] macsypy.search_genes (module) macsypy.search_systems (module) macsypy.system (module), [1] macsypy.system_parser (module) MacsypyError mandatory_genes (macsypy.system.System attribute)

max (macsypy.database.RepliconInfo attribute) max_nb_genes (macsypy.system.System attribute) max_nb_genes() (macsypy.config.Config method) min (macsypy.database.RepliconInfo attribute) min_genes_required (macsypy.system.System attribute) min_genes_required() (macsypy.config.Config method) min_mandatory_genes_required (macsypy.system.System attribute) min_mandatory_genes_required() (macsypy.config.Config method) multi_loci (macsypy.system.System attribute) multi_loci() (macsypy.config.Config method) multi_system (macsypy.gene.Gene attribute)

N

nb_syst_genes (macsypy.search_systems.SystemOccurence attribute)

O

OrderedHMMReport (class in macsypy.report)

output_system_header() (macsypy.search_systems.validSystemHit method)

P

parse() (macsypy.system_parser.SystemParser method) previous_run (macsypy.config.Config attribute) Profile (class in macsypy.gene) profile (macsypy.gene.Gene attribute)

profile_dir (macsypy.config.Config attribute) profile_suffix (macsypy.config.Config attribute) ProfileFactory (class in macsypy.gene) putative_system (macsypy.search_systems.Cluster attribute)

R

replicon_infos() (macsypy.database.RepliconDB method) replicon_names() (macsypy.database.RepliconDB method) replicon_topology (macsypy.config.Config attribute) RepliconDB (class in macsypy.database) RepliconInfo (class in macsypy.database)

report_output() (macsypy.search_systems.systemDetectionReportOrdered method) (macsypy.search_systems.systemDetectionReportUnordered method) res_extract_suffix (macsypy.config.Config attribute) res_search_dir (macsypy.config.Config attribute) res_search_suffix (macsypy.config.Config attribute)

S

save() (macsypy.config.Config method) (macsypy.search_systems.Cluster method) save_extract() (macsypy.report.HMMReport method) search_genes() (in module macsypy.search_genes) search_systems() (in module macsypy.search_systems) sequence_db (macsypy.config.Config attribute) state (macsypy.search_systems.Cluster attribute) (macsypy.search_systems.SystemOccurence attribute) summary_output() (macsypy.search_systems.systemDetectionReportOrdered method) (macsypy.search_systems.systemDetectionReportUnordered method) System (class in macsypy.system) system (macsypy.gene.Gene attribute) system_2_json() (macsypy.search_systems.systemDetectionReportOrdered method)

system_to_parse() (macsypy.system_parser.SystemParser method) SystemBank (class in macsypy.system) SystemDetectionError systemDetectionReportOrdered (class in macsypy.search_systems) systemDetectionReportUnordered (class in macsypy.search_systems) SystemInconsistencyError SystemNameGenerator (class in macsypy.search_systems) SystemOccurence (class in macsypy.search_systems) SystemParser (class in macsypy.system_parser)

T

tabulated_output() (macsypy.search_systems.systemDetectionReportOrdered method) tabulated_output_header() (macsypy.search_systems.systemDetectionReportOrdered method)

topology (macsypy.database.RepliconInfo attribute) topology_file (macsypy.config.Config attribute)

V

validSystemHit (class in macsypy.search_systems)

W

worker_nb (macsypy.config.Config attribute)

working_dir (macsypy.config.Config attribute)