Index

A

add_blast_step() (gene_finder.pipeline.Pipeline method) add_blastn_step() (gene_finder.pipeline.Pipeline method) add_crispr_step() (gene_finder.pipeline.Pipeline method) add_failing() (operon_analyzer.rules.Result method) add_filter_step() (gene_finder.pipeline.Pipeline method) add_passing() (operon_analyzer.rules.Result method) add_seed_step() (gene_finder.pipeline.Pipeline method) add_seed_with_coordinates_step() (gene_finder.pipeline.Pipeline method) alignment (operon_analyzer.repeat_finder.GRFResult property)

AlignmentResult (class in operon_analyzer.spacers) all_features (operon_analyzer.genes.Operon property) all_genes (operon_analyzer.genes.Operon property) analyze() (in module operon_analyzer.analyze) array_length (operon_analyzer.spacers.AlignmentResult property) as_str() (operon_analyzer.genes.Operon method) assemble_operons() (in module operon_analyzer.parse) at_least_n_bp_from_anything() (operon_analyzer.rules.RuleSet method) at_most_n_bp_from_anything() (operon_analyzer.rules.RuleSet method)

B

BrokenSpacer (class in operon_analyzer.piler_parse)

C

cluster_operons_by_feature_order() (in module operon_analyzer.analyze) comp_string (operon_analyzer.spacers.AlignmentResult property) contains_any_set_of_features() (operon_analyzer.rules.RuleSet method) contains_at_least_n_features() (operon_analyzer.rules.RuleSet method) contains_exactly_one_of() (operon_analyzer.rules.RuleSet method) contains_group() (operon_analyzer.rules.RuleSet method)

contig_alignment (operon_analyzer.spacers.AlignmentResult property) contig_end (operon_analyzer.spacers.AlignmentResult property) contig_sequence (operon_analyzer.spacers.AlignmentResult property) contig_start (operon_analyzer.spacers.AlignmentResult property) custom() (operon_analyzer.rules.FilterSet method) (operon_analyzer.rules.RuleSet method)

D

dedup_supersets() (in module operon_analyzer.analyze) deduplicate_operons_approximate() (in module operon_analyzer.analyze)

downstream_sequence (operon_analyzer.repeat_finder.Repeat property) downstream_start (operon_analyzer.repeat_finder.Repeat property)

E

end (operon_analyzer.repeat_finder.GRFResult property) evaluate() (operon_analyzer.rules.FilterSet method) (operon_analyzer.rules.Rule method) (operon_analyzer.rules.RuleSet method)

evaluate_rules_and_reserialize() (in module operon_analyzer.analyze) exclude() (operon_analyzer.rules.RuleSet method)

F

Feature (class in operon_analyzer.genes) feature_names (operon_analyzer.genes.Operon property) feature_region_sequence (operon_analyzer.genes.Operon property)

Filter (class in operon_analyzer.rules) FilterSet (class in operon_analyzer.rules) find_inverted_repeats() (in module operon_analyzer.repeat_finder) find_self_targeting_spacers() (in module operon_analyzer.spacers)

G

gene_finder.pipeline module get() (operon_analyzer.genes.Operon method)

get_unique() (operon_analyzer.genes.Operon method) GRFResult (class in operon_analyzer.repeat_finder) group_similar_operons() (in module operon_analyzer.analyze)

I

is_passing (operon_analyzer.rules.Result property)

L

load_analyzed_operons() (in module operon_analyzer.analyze) load_counts() (in module operon_analyzer.overview)

load_gzipped_operons() (in module operon_analyzer.load) load_operons() (in module operon_analyzer.load) load_sequence() (in module operon_analyzer.load)

M

make_clustered_operon_plots() (in module operon_analyzer.visualize) make_clustered_stacked_operon_plots() (in module operon_analyzer.visualize) match_count (operon_analyzer.spacers.AlignmentResult property) max_distance() (operon_analyzer.rules.RuleSet method) maximum_size() (operon_analyzer.rules.RuleSet method) minimum_size() (operon_analyzer.rules.RuleSet method) module gene_finder.pipeline operon_analyzer.analyze operon_analyzer.genes operon_analyzer.load operon_analyzer.overview operon_analyzer.parse operon_analyzer.piler_parse operon_analyzer.reannotation operon_analyzer.repeat_finder operon_analyzer.rules operon_analyzer.spacers operon_analyzer.visualize

must_be_within_n_bp_of_anything() (operon_analyzer.rules.FilterSet method) must_be_within_n_bp_of_feature() (operon_analyzer.rules.FilterSet method)

O

Operon (class in operon_analyzer.genes) operon_analyzer.analyze module operon_analyzer.genes module operon_analyzer.load module operon_analyzer.overview module operon_analyzer.parse module

operon_analyzer.piler_parse module operon_analyzer.reannotation module operon_analyzer.repeat_finder module operon_analyzer.rules module operon_analyzer.spacers module operon_analyzer.visualize module

P

parse_pilercr_output() (in module operon_analyzer.piler_parse) pick_overlapping_features_by_bit_score() (operon_analyzer.rules.FilterSet method) Pipeline (class in gene_finder.pipeline)

plot_operon_pairs() (in module operon_analyzer.visualize) plot_operons() (in module operon_analyzer.visualize) position (operon_analyzer.piler_parse.BrokenSpacer property) (operon_analyzer.piler_parse.RepeatSpacer property)

R

Repeat (class in operon_analyzer.repeat_finder) repeat_len (operon_analyzer.piler_parse.BrokenSpacer property) (operon_analyzer.piler_parse.RepeatSpacer property) RepeatSpacer (class in operon_analyzer.piler_parse) require() (operon_analyzer.rules.RuleSet method)

Result (class in operon_analyzer.rules) Rule (class in operon_analyzer.rules) RuleSet (class in operon_analyzer.rules) run() (gene_finder.pipeline.Pipeline method) (operon_analyzer.rules.Filter method)

S

same_orientation() (operon_analyzer.rules.RuleSet method) sequence (operon_analyzer.piler_parse.BrokenSpacer property) (operon_analyzer.piler_parse.RepeatSpacer property) SerializableFunction (class in operon_analyzer.rules) set_sequence() (operon_analyzer.genes.Operon method) spacer_alignment (operon_analyzer.spacers.AlignmentResult property)

spacer_len (operon_analyzer.piler_parse.RepeatSpacer property) spacer_order (operon_analyzer.spacers.AlignmentResult property) spacer_sequence (operon_analyzer.spacers.AlignmentResult property) start (operon_analyzer.repeat_finder.GRFResult property) strand (operon_analyzer.spacers.AlignmentResult property) summarize() (in module operon_analyzer.reannotation)

U

upstream_sequence (operon_analyzer.repeat_finder.Repeat property)

upstream_start (operon_analyzer.repeat_finder.Repeat property)