MacSyFinder
User Guide
Developer Guide
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Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
_
__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.Hit 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.gene.CoreGene method)
(macsypy.gene.ModelGene method)
(macsypy.hit.Hit 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.ValidHit method)
(macsypy.model.Model method)
(macsypy.model.ModelBank 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.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)
__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.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_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_node() (macsypy.definition_parser.DefinitionParser method)
_hit_start() (macsypy.report.HMMReport 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)
_profile_features() (macsypy.profile.Profile method)
_replace() (macsypy.database.RepliconInfo method)
_scan_definitions() (macsypy.registries.ModelLocation method)
_scan_profiles() (macsypy.registries.ModelLocation method)
_set_db_type() (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_models() (macsypy.config.Config method)
_set_models_dir() (macsypy.config.Config method)
_set_multi_loci() (macsypy.config.Config method)
_set_replicon_topology() (macsypy.config.Config method)
_set_sequence_db() (macsypy.config.Config method)
_set_topology_file() (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.GembaseHMMReport method)
(macsypy.report.GeneralHMMReport method)
(macsypy.report.HMMReport method)
(macsypy.report.OrderedHMMReport 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)
genes() (macsypy.model.Model property)
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)
getter_maker() (macsypy.system.MetaSetOfHits method)
H
help() (macsypy.package.Package method)
Hit (class in macsypy.hit)
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.config.Config method)
(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() (macsypy.system.System property)
log_level() (macsypy.config.Config method)
loner() (macsypy.gene.ModelGene 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.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)
MatchMaker (class in macsypy.system)
max (macsypy.database.RepliconInfo attribute)
max_nb_genes() (macsypy.config.Config method)
(macsypy.model.Model property)
merge() (macsypy.cluster.Cluster method)
metadata() (macsypy.package.Package property)
MetaSetOfHits (class in macsypy.system)
min (macsypy.database.RepliconInfo attribute)
min_genes_required() (macsypy.config.Config method)
(macsypy.model.Model property)
min_mandatory_genes_required() (macsypy.config.Config method)
(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)
ModelDefinition
ModelGene (class in macsypy.gene)
ModelInconsistencyError
ModelLocation (class in macsypy.registries)
ModelRegistry (class in macsypy.registries)
models() (macsypy.registries.ModelRegistry method)
module
macsypy.cluster
macsypy.config
macsypy.database
macsypy.definition_parser
macsypy.error
macsypy.hit
macsypy.package
macsypy.registries
macsypy.search_genes
macsypy.serialization
macsypy.solution
macsypy.system
macsypy.utils
multi_loci() (macsypy.config.Config method)
(macsypy.model.Model property)
(macsypy.system.System property)
multi_system() (macsypy.gene.ModelGene 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)
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)
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