MacSyFinder
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User Guide
Modeller Guide
Developer Guide
MacSyFinder
Index
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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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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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W
_
__call__() (macsypy.system.MetaSetOfHits method)
__contains__() (macsypy.cluster.Cluster method)
(macsypy.gene.GeneBank method)
__delattr__() (macsypy.hit.HitWeight method)
__eq__() (macsypy.hit.CoreHit method)
(macsypy.hit.HitWeight method)
(macsypy.hit.ModelHit method)
__getitem__() (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.HitWeight method)
(macsypy.hit.ModelHit method)
__init__() (macsypy.cluster.Cluster method)
(macsypy.config.Config method)
(macsypy.config.MacsyDefaults 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.HitWeight method)
(macsypy.hit.Loner method)
(macsypy.hit.LonerMultiSystem method)
(macsypy.hit.ModelHit method)
(macsypy.hit.MultiSystem method)
(macsypy.model_conf_parser.ModelConfParser 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.gene.GeneBank method)
__lt__() (macsypy.hit.CoreHit method)
(macsypy.hit.ModelHit method)
__repr__() (macsypy.hit.HitWeight method)
__setattr__() (macsypy.hit.HitWeight method)
__str__() (macsypy.cluster.Cluster method)
(macsypy.gene.ModelGene method)
(macsypy.hit.AbstractCounterpartHit method)
(macsypy.hit.CoreHit method)
(macsypy.hit.ModelHit 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.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.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)
_check_replicon_consistency() (macsypy.cluster.Cluster method)
_config_file_2_dict() (macsypy.config.Config method)
_create_exchangeable_map() (macsypy.system.MatchMaker method)
_get_model_conf_node() (macsypy.model_conf_parser.ModelConfParser method)
_parse_section() (macsypy.model_conf_parser.ModelConfParser 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
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)
F
forbidden_hits (macsypy.system.AbstractUnordered property)
fulfilled_function() (macsypy.cluster.Cluster method)
(macsypy.system.AbstractClusterizedHits method)
functions (macsypy.cluster.Cluster property)
G
GeneBank (class in macsypy.gene)
genes_fqn() (macsypy.gene.GeneBank method)
GeneStatus (class in macsypy.gene)
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)
getter_maker() (macsypy.system.MetaSetOfHits method)
H
hit (macsypy.hit.ModelHit property)
hit_weights (macsypy.cluster.Cluster property)
hit_weights() (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)
I
inter_gene_max_space (macsypy.gene.ModelGene property)
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 property)
(macsypy.gene.ModelGene property)
is_forbidden() (macsypy.gene.ModelGene method)
is_mandatory() (macsypy.gene.ModelGene 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.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_nb_genes() (macsypy.config.Config method)
merge() (macsypy.cluster.Cluster method)
MetaSetOfHits (class in macsypy.system)
min_genes_required() (macsypy.config.Config method)
min_mandatory_genes_required() (macsypy.config.Config method)
Model
model (macsypy.gene.ModelGene property)
Model family
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)
module
macsypy.error
macsypy.model_conf_parser
multi_loci (macsypy.system.System property)
multi_loci() (macsypy.config.Config method)
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
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 (macsypy.gene.CoreGene property)
pyproject.toml
R
README.md
reasons (macsypy.system.UnlikelySystem property)
RejectedCandidate (class in macsypy.system)
replace() (macsypy.cluster.Cluster method)
replicon_name (macsypy.cluster.Cluster property)
(macsypy.system.AbstractSetOfHits property)
S
save() (macsypy.config.Config 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
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)
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