Silvio
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Silvio
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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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K
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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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W
_
_abc_impl (silvio.catalog.RecExpSim.RecExperiment attribute)
(silvio.catalog.RecExpSim.RecHost attribute)
(silvio.events.Event attribute)
(silvio.experiment.Experiment attribute)
(silvio.extensions.all_events.AlterGeneExpressionEvent attribute)
(silvio.extensions.all_events.AlterGenePromoterEvent attribute)
(silvio.extensions.all_events.InsertGeneEvent attribute)
(silvio.extensions.all_events.RemoveGeneEvent attribute)
(silvio.extensions.modules.genome_expression.GenomeExpression attribute)
(silvio.extensions.modules.genome_library.GenomeLibrary attribute)
(silvio.extensions.modules.genome_list.GenomeList attribute)
(silvio.extensions.modules.growth_behaviour.GrowthBehaviour attribute)
(silvio.extensions.modules.metabolic_flux.MetabolicFlux attribute)
(silvio.extensions.modules.phenotype_size.PhenotypeSize attribute)
(silvio.extensions.records.gene.crafted_gene.CraftedGene attribute)
(silvio.extensions.records.gene.gene.Gene attribute)
(silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
(silvio.extensions.records.gene.stub_gene.StubGene attribute)
(silvio.extensions.records.growth_record.GrowthOutcome attribute)
(silvio.extensions.sets.shotgun_sequencing.assembly.ContigAssembler attribute)
(silvio.extensions.sets.shotgun_sequencing.assembly.GreedyContigAssembler attribute)
(silvio.extensions.sets.shotgun_sequencing.assembly.RandomContigAssembler attribute)
(silvio.host.Host attribute)
(silvio.module.Module attribute)
(silvio.record.Record attribute)
_asdict() (silvio.extensions.modules.genome_library.PrimerMatch method)
(silvio.extensions.sets.shotgun_sequencing.assembly.PairwiseScore method)
(silvio.extensions.sets.shotgun_sequencing.datatype.LocalizedSequence method)
(silvio.extensions.sets.shotgun_sequencing.datatype.Scaffold method)
(silvio.host.ListenerEntry method)
_field_defaults (silvio.extensions.modules.genome_library.PrimerMatch attribute)
(silvio.extensions.sets.shotgun_sequencing.assembly.PairwiseScore attribute)
(silvio.extensions.sets.shotgun_sequencing.datatype.LocalizedSequence attribute)
(silvio.extensions.sets.shotgun_sequencing.datatype.Scaffold attribute)
(silvio.host.ListenerEntry attribute)
_fields (silvio.extensions.modules.genome_library.PrimerMatch attribute)
(silvio.extensions.sets.shotgun_sequencing.assembly.PairwiseScore attribute)
(silvio.extensions.sets.shotgun_sequencing.datatype.LocalizedSequence attribute)
(silvio.extensions.sets.shotgun_sequencing.datatype.Scaffold attribute)
(silvio.host.ListenerEntry attribute)
_make() (silvio.extensions.modules.genome_library.PrimerMatch class method)
(silvio.extensions.sets.shotgun_sequencing.assembly.PairwiseScore class method)
(silvio.extensions.sets.shotgun_sequencing.datatype.LocalizedSequence class method)
(silvio.extensions.sets.shotgun_sequencing.datatype.Scaffold class method)
(silvio.host.ListenerEntry class method)
_replace() (silvio.extensions.modules.genome_library.PrimerMatch method)
(silvio.extensions.sets.shotgun_sequencing.assembly.PairwiseScore method)
(silvio.extensions.sets.shotgun_sequencing.datatype.LocalizedSequence method)
(silvio.extensions.sets.shotgun_sequencing.datatype.Scaffold method)
(silvio.host.ListenerEntry method)
A
alldef() (in module silvio.utils)
alter_sequence() (silvio.extensions.modules.genome_library.GenomeLibrary method)
AlterGeneExpressionEvent (class in silvio.extensions.all_events)
AlterGenePromoterEvent (class in silvio.extensions.all_events)
apply() (silvio.extensions.sets.shotgun_sequencing.assembly.ContigAssembler method)
(silvio.extensions.sets.shotgun_sequencing.assembly.GreedyContigAssembler method)
(silvio.extensions.sets.shotgun_sequencing.assembly.RandomContigAssembler method)
(silvio.extensions.sets.shotgun_sequencing.sequencing.ShotgunSequencer method)
apply_internal() (silvio.extensions.sets.shotgun_sequencing.assembly.ContigAssembler method)
(silvio.extensions.sets.shotgun_sequencing.assembly.GreedyContigAssembler method)
(silvio.extensions.sets.shotgun_sequencing.assembly.RandomContigAssembler method)
as_consensus_sequence() (silvio.extensions.sets.shotgun_sequencing.datatype.EstimatedSequence method)
B
bind() (silvio.extensions.modules.genome_expression.GenomeExpression method)
(silvio.extensions.modules.genome_library.GenomeLibrary method)
(silvio.extensions.modules.genome_list.GenomeList method)
(silvio.extensions.modules.growth_behaviour.GrowthBehaviour method)
(silvio.extensions.modules.metabolic_flux.MetabolicFlux method)
(silvio.extensions.modules.phenotype_size.PhenotypeSize method)
(silvio.module.Module method)
bind_host() (silvio.experiment.Experiment method)
build_clone_attrs() (silvio.host.Host method)
build_ecol_host() (silvio.catalog.RecExpSim.RecExperiment method)
build_pput_host() (silvio.catalog.RecExpSim.RecExperiment method)
C
calc_fast_wrong_prom_expr() (silvio.extensions.modules.genome_expression.GenomeExpression method)
Calc_MaxExpress() (silvio.extensions.modules.growth_behaviour.GrowthBehaviour method)
calc_num_scaffolds_obtained() (silvio.extensions.sets.shotgun_sequencing.sequencing.ShotgunSequencer method)
calc_primer_matches() (silvio.extensions.modules.genome_library.GenomeLibrary method)
calc_prom_str() (silvio.extensions.modules.genome_expression.GenomeExpression method)
calc_sequence_score() (in module silvio.extensions.sets.shotgun_sequencing.evaluation)
calc_shannon_entropy() (silvio.extensions.sets.shotgun_sequencing.datatype.EstimatedSequence method)
calc_total_score() (in module silvio.extensions.sets.shotgun_sequencing.evaluation)
check_primer_integrity() (in module silvio.extensions.modules.genome_library)
check_primer_integrity_and_recombination() (in module silvio.extensions.utils.misc)
clone() (silvio.extensions.records.growth_record.GrowthOutcome method)
(silvio.registry.Registry method)
clone_with_recombination() (silvio.catalog.RecExpSim.RecExperiment method)
coalesce() (in module silvio.utils)
combine_data() (in module silvio.outcome)
ContigAssembler (class in silvio.extensions.sets.shotgun_sequencing.assembly)
convert_to_seqrecord() (in module silvio.extensions.sets.shotgun_sequencing.sequencing)
copy() (silvio.catalog.RecExpSim.RecHost method)
(silvio.extensions.modules.genome_expression.GenomeExpression method)
(silvio.extensions.modules.genome_library.GenomeLibrary method)
(silvio.extensions.modules.genome_list.GenomeList method)
(silvio.extensions.modules.growth_behaviour.GrowthBehaviour method)
(silvio.extensions.modules.metabolic_flux.MetabolicFlux method)
(silvio.extensions.modules.phenotype_size.PhenotypeSize method)
(silvio.host.Host method)
(silvio.module.Module method)
CraftedGene (class in silvio.extensions.records.gene.crafted_gene)
create_host() (silvio.catalog.RecExpSim.RecExperiment method)
D
DATADIR (in module silvio.config)
DataOutcome (class in silvio.outcome)
DataWithPlotOutcome (class in silvio.outcome)
display_data() (silvio.outcome.DataOutcome method)
display_plot() (silvio.outcome.DataWithPlotOutcome method)
E
emit() (silvio.host.Host method)
end_loc (silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
error (silvio.outcome.Outcome attribute)
ErrorRate() (in module silvio.extensions.utils.laboratory)
estimate_from_overlap() (in module silvio.extensions.sets.shotgun_sequencing.datatype)
EstimatedSequence (class in silvio.extensions.sets.shotgun_sequencing.datatype)
evaluate_sequence() (in module silvio.extensions.sets.shotgun_sequencing.evaluation)
Event (class in silvio.events)
EventEmitter (in module silvio.events)
EventLogger (in module silvio.events)
evtype (silvio.host.ListenerEntry attribute)
expected_len (silvio.extensions.sets.shotgun_sequencing.datatype.Scaffold attribute)
Experiment (class in silvio.experiment)
ExperimentException
export_data() (silvio.outcome.DataOutcome method)
export_plot() (silvio.outcome.DataWithPlotOutcome method)
F
find_best_primer_match() (in module silvio.extensions.modules.genome_library)
find_gene_or_abort() (silvio.catalog.RecExpSim.RecHost method)
find_host_or_abort() (silvio.catalog.RecExpSim.RecExperiment method)
first() (in module silvio.utils)
G
Gene (class in silvio.extensions.records.gene.gene)
Generator (class in silvio.random)
genes (silvio.extensions.modules.genome_library.GenomeLibrary attribute)
GenomeExpression (class in silvio.extensions.modules.genome_expression)
GenomeLibrary (class in silvio.extensions.modules.genome_library)
GenomeList (class in silvio.extensions.modules.genome_list)
get_consensus_from_overlap() (in module silvio.extensions.sets.shotgun_sequencing.datatype)
get_genes_by_name() (silvio.extensions.modules.genome_library.GenomeLibrary method)
(silvio.extensions.modules.genome_list.GenomeList method)
GreedyContigAssembler (class in silvio.extensions.sets.shotgun_sequencing.assembly)
Growth_Maxrate() (in module silvio.extensions.utils.misc)
GrowthBehaviour (class in silvio.extensions.modules.growth_behaviour)
GrowthOutcome (class in silvio.catalog.RecExpSim)
(class in silvio.extensions.records.growth_record)
H
has_error() (silvio.outcome.Outcome method)
Help_GrowthConstant() (in module silvio.extensions.utils.misc)
Help_Progressbar() (in module silvio.extensions.utils.visual)
Help_PromoterStrength() (in module silvio.extensions.utils.misc)
Host (class in silvio.host)
HostException
I
i (silvio.extensions.sets.shotgun_sequencing.assembly.PairwiseScore attribute)
insert() (silvio.registry.Registry method)
insert_gene() (silvio.catalog.RecExpSim.RecHost method)
(silvio.extensions.modules.genome_library.GenomeLibrary method)
InsertGeneEvent (class in silvio.extensions.all_events)
K
k (silvio.extensions.sets.shotgun_sequencing.assembly.PairwiseScore attribute)
L
list_integer() (in module silvio.extensions.utils.transform)
list_onehot() (in module silvio.extensions.utils.transform)
listen_alter_gene_expression() (silvio.extensions.modules.metabolic_flux.MetabolicFlux method)
listen_alter_gene_promoter() (silvio.extensions.modules.genome_expression.GenomeExpression method)
(silvio.extensions.modules.genome_library.GenomeLibrary method)
(silvio.extensions.modules.genome_list.GenomeList method)
listen_insert_gene() (silvio.extensions.modules.genome_library.GenomeLibrary method)
(silvio.extensions.modules.genome_list.GenomeList method)
(silvio.extensions.modules.metabolic_flux.MetabolicFlux method)
(silvio.extensions.modules.phenotype_size.PhenotypeSize method)
listen_remove_gene() (silvio.extensions.modules.genome_library.GenomeLibrary method)
(silvio.extensions.modules.genome_list.GenomeList method)
(silvio.extensions.modules.metabolic_flux.MetabolicFlux method)
(silvio.extensions.modules.phenotype_size.PhenotypeSize method)
ListenerEntry (class in silvio.host)
loc_end (silvio.extensions.modules.genome_library.PrimerMatch attribute)
loc_start (silvio.extensions.modules.genome_library.PrimerMatch attribute)
LocalizedGene (class in silvio.extensions.records.gene.localized_gene)
LocalizedSequence (class in silvio.extensions.sets.shotgun_sequencing.datatype)
locus (silvio.extensions.sets.shotgun_sequencing.datatype.LocalizedSequence attribute)
log() (silvio.host.Host method)
M
make() (silvio.catalog.RecExpSim.RecHost method)
(silvio.extensions.modules.genome_expression.GenomeExpression method)
(silvio.extensions.modules.genome_library.GenomeLibrary method)
(silvio.extensions.modules.genome_list.GenomeList method)
(silvio.extensions.modules.growth_behaviour.GrowthBehaviour method)
(silvio.extensions.modules.metabolic_flux.MetabolicFlux method)
(silvio.extensions.modules.phenotype_size.PhenotypeSize method)
(silvio.host.Host method)
(silvio.module.Module method)
make_background_seq() (in module silvio.extensions.modules.genome_library)
make_generator() (silvio.host.Host method)
(silvio.tool.Tool method)
make_plot() (silvio.catalog.RecExpSim.GrowthOutcome method)
(silvio.outcome.DataWithPlotOutcome method)
Make_ProductionExperiment() (silvio.extensions.modules.growth_behaviour.GrowthBehaviour method)
Make_TempGrowthExp() (silvio.extensions.modules.growth_behaviour.GrowthBehaviour method)
make_variant() (silvio.extensions.records.gene.crafted_gene.CraftedGene method)
match() (in module silvio.extensions.sets.shotgun_sequencing.assembly)
measure_promoter_strength() (silvio.catalog.RecExpSim.RecExperiment method)
MetabolicFlux (class in silvio.extensions.modules.metabolic_flux)
Module (class in silvio.module)
ModuleException
N
name (silvio.extensions.records.gene.crafted_gene.CraftedGene attribute)
(silvio.extensions.records.gene.gene.Gene attribute)
(silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
(silvio.extensions.records.gene.stub_gene.StubGene attribute)
numtochar() (in module silvio.extensions.sets.shotgun_sequencing.visualization)
O
observe() (silvio.host.Host method)
optimize() (silvio.extensions.modules.metabolic_flux.MetabolicFlux method)
orf (silvio.extensions.records.gene.crafted_gene.CraftedGene attribute)
(silvio.extensions.records.gene.gene.Gene attribute)
(silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
(silvio.extensions.records.gene.stub_gene.StubGene attribute)
orf_len (silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
Outcome (class in silvio.outcome)
P
PairwiseScore (class in silvio.extensions.sets.shotgun_sequencing.assembly)
PhenotypeSize (class in silvio.extensions.modules.phenotype_size)
phred_to_prob() (in module silvio.extensions.sets.shotgun_sequencing.sequencing)
pick_choices() (in module silvio.random)
(silvio.random.Generator method)
pick_exponential() (in module silvio.random)
(silvio.random.Generator method)
pick_integer() (in module silvio.random)
(silvio.random.Generator method)
pick_normal() (in module silvio.random)
(silvio.random.Generator method)
pick_samples() (in module silvio.random)
(silvio.random.Generator method)
pick_seed() (in module silvio.random)
(silvio.random.Generator method)
pick_uniform() (in module silvio.random)
(silvio.random.Generator method)
PrimerMatch (class in silvio.extensions.modules.genome_library)
print_assembly_evaluation() (in module silvio.extensions.sets.shotgun_sequencing.visualization)
print_estimation_evaluation() (in module silvio.extensions.sets.shotgun_sequencing.visualization)
print_evaluation_alignment() (in module silvio.extensions.sets.shotgun_sequencing.visualization)
print_event_log() (silvio.host.Host method)
print_scaffold() (in module silvio.extensions.sets.shotgun_sequencing.visualization)
print_scaffold_as_fastq() (in module silvio.extensions.sets.shotgun_sequencing.visualization)
print_status() (silvio.catalog.RecExpSim.RecExperiment method)
(silvio.catalog.RecExpSim.RecHost method)
prom (silvio.extensions.records.gene.crafted_gene.CraftedGene attribute)
(silvio.extensions.records.gene.gene.Gene attribute)
(silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
(silvio.extensions.records.gene.stub_gene.StubGene attribute)
prom_len (silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
R
r1_seqrecord (silvio.extensions.sets.shotgun_sequencing.datatype.Scaffold attribute)
r2_seqrecord (silvio.extensions.sets.shotgun_sequencing.datatype.Scaffold attribute)
RandomContigAssembler (class in silvio.extensions.sets.shotgun_sequencing.assembly)
RatedSequence (class in silvio.extensions.sets.shotgun_sequencing.sequencing)
RecExperiment (class in silvio.catalog.RecExpSim)
RecHost (class in silvio.catalog.RecExpSim)
Record (class in silvio.record)
ref_prom (silvio.catalog.RecExpSim.RecHost attribute)
Registry (class in silvio.registry)
RemoveGeneEvent (class in silvio.extensions.all_events)
run (silvio.host.ListenerEntry attribute)
S
Scaffold (class in silvio.extensions.sets.shotgun_sequencing.datatype)
score (silvio.extensions.sets.shotgun_sequencing.assembly.PairwiseScore attribute)
seq (silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
sequence (silvio.extensions.sets.shotgun_sequencing.datatype.LocalizedSequence attribute)
Sequence_ReferenceDistance() (in module silvio.extensions.utils.misc)
set_seed() (in module silvio.random)
ShotgunSequencer (class in silvio.extensions.sets.shotgun_sequencing.sequencing)
silvio (module)
silvio.catalog (module)
silvio.catalog.RecExpSim (module)
silvio.config (module)
silvio.events (module)
silvio.experiment (module)
silvio.extensions (module)
silvio.extensions.all_events (module)
silvio.extensions.common (module)
silvio.extensions.modules (module)
silvio.extensions.modules.genome_expression (module)
silvio.extensions.modules.genome_library (module)
silvio.extensions.modules.genome_list (module)
silvio.extensions.modules.growth_behaviour (module)
silvio.extensions.modules.metabolic_flux (module)
silvio.extensions.modules.phenotype_size (module)
silvio.extensions.records (module)
silvio.extensions.records.gene (module)
silvio.extensions.records.gene.crafted_gene (module)
silvio.extensions.records.gene.gene (module)
silvio.extensions.records.gene.localized_gene (module)
silvio.extensions.records.gene.stub_gene (module)
silvio.extensions.records.growth_record (module)
silvio.extensions.sets (module)
silvio.extensions.sets.shotgun_sequencing (module)
silvio.extensions.sets.shotgun_sequencing.assembly (module)
silvio.extensions.sets.shotgun_sequencing.datatype (module)
silvio.extensions.sets.shotgun_sequencing.evaluation (module)
silvio.extensions.sets.shotgun_sequencing.sequencing (module)
silvio.extensions.sets.shotgun_sequencing.storage (module)
silvio.extensions.sets.shotgun_sequencing.visualization (module)
silvio.extensions.tools (module)
silvio.extensions.tools.shotgun_sequencing (module)
silvio.extensions.utils (module)
silvio.extensions.utils.laboratory (module)
silvio.extensions.utils.misc (module)
silvio.extensions.utils.shotgun_sequencing (module)
silvio.extensions.utils.transform (module)
silvio.extensions.utils.visual (module)
silvio.host (module)
silvio.module (module)
silvio.outcome (module)
silvio.random (module)
silvio.record (module)
silvio.registry (module)
silvio.tool (module)
silvio.utils (module)
simulate_growth() (silvio.catalog.RecExpSim.RecExperiment method)
simulate_vaccine_production() (silvio.catalog.RecExpSim.RecExperiment method)
SimulationException
spend_budget_or_abort() (silvio.catalog.RecExpSim.RecExperiment method)
start_loc (silvio.extensions.records.gene.localized_gene.LocalizedGene attribute)
StubGene (class in silvio.extensions.records.gene.stub_gene)
succeeded() (silvio.outcome.Outcome method)
success (silvio.extensions.modules.genome_library.PrimerMatch attribute)
sync() (silvio.catalog.RecExpSim.RecHost method)
(silvio.extensions.modules.genome_expression.GenomeExpression method)
(silvio.extensions.modules.genome_library.GenomeLibrary method)
(silvio.extensions.modules.genome_list.GenomeList method)
(silvio.extensions.modules.growth_behaviour.GrowthBehaviour method)
(silvio.extensions.modules.metabolic_flux.MetabolicFlux method)
(silvio.extensions.modules.phenotype_size.PhenotypeSize method)
(silvio.host.Host method)
(silvio.module.Module method)
sync_modules() (silvio.host.Host method)
T
Tool (class in silvio.tool)
ToolException
W
write_scaffolds_to_file() (in module silvio.extensions.sets.shotgun_sequencing.storage)
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