Index

_

__add__() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) __author__ (in module rna_library) __email__ (in module rna_library) __eq__() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) __getitem__() (rna_library.JunctionEntry method) (rna_library.processing.junction_data.JunctionEntry method) (rna_library.processing.JunctionEntry method) __iter__() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method)

__str__() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) __version__ (in module rna_library) _CACHE (in module rna_library.core.folding), [1] _CACHE_FILE (in module rna_library.core.folding) _CURRENT_SIZE (in module rna_library.core.folding) _DEFAULT_PARAMS (in module rna_library.core.folding) _get_ids_internal() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) _LAST_SIZE (in module rna_library.core.folding)

A

A (rna_library.core.enums.Nucleotide attribute) (rna_library.core.Nucleotide attribute) (rna_library.Nucleotide attribute) add_child() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) add_data() (rna_library.processing.normalize.OptimizeJunction method)

add_reactivity() (in module rna_library.processing.row_utils) ALLOWED_PAIRS (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums) AU (rna_library.BasePair attribute) (rna_library.core.BasePair attribute) (rna_library.core.enums.BasePair attribute)

B

BasePair (class in rna_library) (class in rna_library.core) (class in rna_library.core.enums) BASEPAIR_MAPPER (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums) bind() (rna_library.JunctionData method) (rna_library.processing.junction_data.JunctionData method) (rna_library.processing.JunctionData method) block_commons() (in module rna_library.processing.row_utils) bp_codes_to_sequence() (in module rna_library.core.util) BP_VALS (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums) BPS (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums) buffer() (rna_library.Hairpin method) (rna_library.Helix method) (rna_library.Junction method) (rna_library.Motif method) (rna_library.SingleStrand method) (rna_library.structure.Hairpin method) (rna_library.structure.hairpin.Hairpin method) (rna_library.structure.Helix method) (rna_library.structure.helix.Helix method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) (rna_library.structure.SingleStrand method) (rna_library.structure.singlestrand.SingleStrand method)

build_barcodes() (in module rna_library) (in module rna_library.design) (in module rna_library.design.barcode) build_motif_df() (in module rna_library) (in module rna_library.processing) (in module rna_library.processing.process_histos) build_react_df() (in module rna_library) (in module rna_library.processing) (in module rna_library.processing.process_histos)

C

C (rna_library.core.enums.Nucleotide attribute) (rna_library.core.Nucleotide attribute) (rna_library.Nucleotide attribute) CG (rna_library.BasePair attribute) (rna_library.core.BasePair attribute) (rna_library.core.enums.BasePair attribute) change_motif() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) check_pairs() (in module rna_library.design.barcode) children() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method)

closing_pairs() (rna_library.Junction method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) collect_junction_entries() (in module rna_library.processing.row_utils) connectivity_list() (in module rna_library.core) (in module rna_library.core.util) contains() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) contains_jct() (in module rna_library.design.barcode)

D

depth() (rna_library.Motif method), [1] (rna_library.structure.Motif method), [1] (rna_library.structure.motif.Motif method), [1] display() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method)

dms_active_idxs() (rna_library.Junction method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) dsci() (in module rna_library.core) (in module rna_library.core.util)

E

end_pos() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method)

EXCESS_MAPPER (in module rna_library.processing.stats)

F

fold_cache() (in module rna_library.core) (in module rna_library.core.folding) folding_params() (in module rna_library.core) (in module rna_library.core.folding)

FoldResult (in module rna_library.core) (in module rna_library.core.folding)

G

G (rna_library.core.enums.Nucleotide attribute) (rna_library.core.Nucleotide attribute) (rna_library.Nucleotide attribute) gaps() (rna_library.Junction method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) GC (rna_library.BasePair attribute) (rna_library.core.BasePair attribute) (rna_library.core.enums.BasePair attribute) generate_sequences() (in module rna_library.design.barcode) (rna_library.Hairpin method) (rna_library.Helix method) (rna_library.Junction method) (rna_library.Motif method) (rna_library.SingleStrand method) (rna_library.structure.Hairpin method) (rna_library.structure.hairpin.Hairpin method) (rna_library.structure.Helix method) (rna_library.structure.helix.Helix method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) (rna_library.structure.SingleStrand method) (rna_library.structure.singlestrand.SingleStrand method) get() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method)

get_active_data() (rna_library.JunctionData method) (rna_library.processing.junction_data.JunctionData method) (rna_library.processing.JunctionData method) get_helix() (in module rna_library.structure.parser) get_ids() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) get_idxs() (in module rna_library.design.barcode) get_junction_or_hairpin() (in module rna_library.structure.parser) get_motif() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) get_motifs() (in module rna_library.structure.parser) get_pair_list() (in module rna_library.core.util) get_sequence_structure() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) get_singlestrand() (in module rna_library.structure.parser) get_substructure() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) GU (rna_library.BasePair attribute) (rna_library.core.BasePair attribute) (rna_library.core.enums.BasePair attribute)

H

Hairpin (class in rna_library) (class in rna_library.structure) (class in rna_library.structure.hairpin) HAIRPIN (rna_library.core.enums.MotifType attribute) (rna_library.core.MotifType attribute) (rna_library.MotifType attribute) hairpins() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) has_children() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) has_non_canonical() (rna_library.Hairpin method) (rna_library.Helix method) (rna_library.Junction method) (rna_library.Motif method) (rna_library.SingleStrand method) (rna_library.structure.Hairpin method) (rna_library.structure.hairpin.Hairpin method) (rna_library.structure.Helix method) (rna_library.structure.helix.Helix method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) (rna_library.structure.SingleStrand method) (rna_library.structure.singlestrand.SingleStrand method)

has_parent() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) Helix (class in rna_library) (class in rna_library.structure) (class in rna_library.structure.helix) HELIX (rna_library.core.enums.MotifType attribute) (rna_library.core.MotifType attribute) (rna_library.MotifType attribute) helix() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) helix_length() (in module rna_library.structure.parser) helix_replace_() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) highest_id() (in module rna_library) (in module rna_library.structure) (in module rna_library.structure.motif)

I

id() (rna_library.Motif method), [1] (rna_library.structure.Motif method), [1] (rna_library.structure.motif.Motif method), [1] InvalidArgument, [1] InvalidDotBracket, [1] iqr_excess() (in module rna_library.processing.stats) is_AU() (rna_library.BasePair method) (rna_library.core.BasePair method) (rna_library.core.enums.BasePair method) is_barcode() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) is_canoncial() (rna_library.BasePair method) (rna_library.core.BasePair method) (rna_library.core.enums.BasePair method) is_circular() (in module rna_library.core) (in module rna_library.core.util) is_GC() (rna_library.BasePair method) (rna_library.core.BasePair method) (rna_library.core.enums.BasePair method) is_GU() (rna_library.BasePair method) (rna_library.core.BasePair method) (rna_library.core.enums.BasePair method) is_hairpin() (rna_library.Hairpin method) (rna_library.Motif method) (rna_library.structure.Hairpin method) (rna_library.structure.hairpin.Hairpin method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method)

is_helix() (rna_library.Helix method) (rna_library.Motif method) (rna_library.structure.Helix method) (rna_library.structure.helix.Helix method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) is_junction() (rna_library.Junction method) (rna_library.Motif method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) is_singlestrand() (rna_library.Motif method) (rna_library.SingleStrand method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) (rna_library.structure.SingleStrand method) (rna_library.structure.singlestrand.SingleStrand method) is_symmetrical() (in module rna_library.core) (in module rna_library.core.util) (rna_library.JunctionData method) (rna_library.JunctionEntry method) (rna_library.processing.junction_data.JunctionData method) (rna_library.processing.junction_data.JunctionEntry method) (rna_library.processing.JunctionData method) (rna_library.processing.JunctionEntry method) itermotifs() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method)

J

Junction (class in rna_library) (class in rna_library.structure) (class in rna_library.structure.junction) JUNCTION (rna_library.core.enums.MotifType attribute) (rna_library.core.MotifType attribute) (rna_library.MotifType attribute) JunctionData (class in rna_library) (class in rna_library.processing) (class in rna_library.processing.junction_data)

JunctionEntry (class in rna_library) (class in rna_library.processing) (class in rna_library.processing.junction_data) junctions() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method)

K

key() (rna_library.JunctionEntry method) (rna_library.processing.junction_data.JunctionEntry method) (rna_library.processing.JunctionEntry method)

L

LEGAL_BPS (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums) link_children() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method)

load_fasta() (in module rna_library.core) (in module rna_library.core.util) longest_repeat() (in module rna_library.design.barcode)

M

mad_excess() (in module rna_library.processing.stats) make_sequences() (in module rna_library.design.barcode) measure_variance() (rna_library.JunctionData method) (rna_library.processing.junction_data.JunctionData method) (rna_library.processing.JunctionData method) MissingDependency, [1] module rna_library rna_library.core rna_library.core.enums rna_library.core.error rna_library.core.folding rna_library.core.util rna_library.design rna_library.design.barcode rna_library.design.library rna_library.processing rna_library.processing.junction_data rna_library.processing.normalize rna_library.processing.process_histos rna_library.processing.row_utils rna_library.processing.stats rna_library.structure rna_library.structure.hairpin rna_library.structure.helix rna_library.structure.junction rna_library.structure.motif rna_library.structure.parser rna_library.structure.secstruct rna_library.structure.singlestrand

Motif (class in rna_library) (class in rna_library.structure) (class in rna_library.structure.motif) motif_replace_() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) MotifType (class in rna_library) (class in rna_library.core) (class in rna_library.core.enums)

N

normalize_coeff_fit() (in module rna_library) (in module rna_library.processing) (in module rna_library.processing.normalize) normalize_hairpin() (in module rna_library) (in module rna_library.processing) (in module rna_library.processing.normalize) NormJob (in module rna_library.processing.normalize) nt_codes_to_sequences() (in module rna_library.core.util) NT_VALS (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums) NTS (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums)

Nucleotide (class in rna_library) (class in rna_library.core) (class in rna_library.core.enums) NUCLEOTIDE_MAPPER (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums) num_reads() (in module rna_library.processing.row_utils) number_branches() (rna_library.Junction method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) number_sequences() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method)

O

OptimizeJunction (class in rna_library.processing.normalize)

P

pairs() (rna_library.Helix method) (rna_library.structure.Helix method) (rna_library.structure.helix.Helix method) parent() (rna_library.Motif method), [1] (rna_library.structure.Motif method), [1] (rna_library.structure.motif.Motif method), [1] parse_to_motifs() (in module rna_library) (in module rna_library.structure) (in module rna_library.structure.parser)

plot() (rna_library.JunctionData method) (rna_library.processing.junction_data.JunctionData method) (rna_library.processing.JunctionData method) pool_with_distance() (in module rna_library.core.util) process_histos() (in module rna_library.processing) (in module rna_library.processing.process_histos)

R

rebuild_data() (rna_library.JunctionData method) (rna_library.processing.junction_data.JunctionData method) (rna_library.processing.JunctionData method) recursive_sequence() (rna_library.Hairpin method) (rna_library.Helix method) (rna_library.Junction method) (rna_library.Motif method) (rna_library.SingleStrand method) (rna_library.structure.Hairpin method) (rna_library.structure.hairpin.Hairpin method) (rna_library.structure.Helix method) (rna_library.structure.helix.Helix method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) (rna_library.structure.SingleStrand method) (rna_library.structure.singlestrand.SingleStrand method) recursive_structure() (rna_library.Hairpin method) (rna_library.Helix method) (rna_library.Junction method) (rna_library.Motif method) (rna_library.SingleStrand method) (rna_library.structure.Hairpin method) (rna_library.structure.hairpin.Hairpin method) (rna_library.structure.Helix method) (rna_library.structure.helix.Helix method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) (rna_library.structure.SingleStrand method) (rna_library.structure.singlestrand.SingleStrand method) rna_library module rna_library.core module rna_library.core.enums module rna_library.core.error module

rna_library.core.folding module rna_library.core.util module rna_library.design module rna_library.design.barcode module rna_library.design.library module rna_library.processing module rna_library.processing.junction_data module rna_library.processing.normalize module rna_library.processing.process_histos module rna_library.processing.row_utils module rna_library.processing.stats module rna_library.structure module rna_library.structure.hairpin module rna_library.structure.helix module rna_library.structure.junction module rna_library.structure.motif module rna_library.structure.parser module rna_library.structure.secstruct module rna_library.structure.singlestrand module row_normalize_hairpin() (in module rna_library.processing.row_utils)

S

safe_mkdir() (in module rna_library.core) (in module rna_library.core.util) safe_rm() (in module rna_library.core) (in module rna_library.core.util) same_pattern() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) satisfies_constraints() (in module rna_library.core.util) save_cache() (in module rna_library.core) (in module rna_library.core.folding) score() (in module rna_library.processing.row_utils) SecStruct (class in rna_library) (class in rna_library.structure) (class in rna_library.structure.secstruct) sequence() (rna_library.Motif method), [1] (rna_library.SecStruct property) (rna_library.structure.Motif method), [1] (rna_library.structure.motif.Motif method), [1] (rna_library.structure.SecStruct property) (rna_library.structure.secstruct.SecStruct property) sequences() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) set_barcode() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) set_children() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) set_ids_() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) set_sequence() (in module rna_library.design.barcode) (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method)

show() (rna_library.JunctionData method) (rna_library.processing.junction_data.JunctionData method) (rna_library.processing.JunctionData method) sigma_excess() (in module rna_library.processing.stats) sigma_excess_normed() (in module rna_library.processing.stats) signal_to_noise() (in module rna_library.processing.row_utils) SingleStrand (class in rna_library) (class in rna_library.structure) (class in rna_library.structure.singlestrand) SINGLESTRAND (rna_library.core.enums.MotifType attribute) (rna_library.core.MotifType attribute) (rna_library.MotifType attribute) singlestrands() (rna_library.SecStruct method) (rna_library.structure.SecStruct method) (rna_library.structure.secstruct.SecStruct method) size() (rna_library.Helix method), [1] (rna_library.structure.Helix method), [1] (rna_library.structure.helix.Helix method), [1] spread() (rna_library.processing.normalize.OptimizeJunction method) start_pos() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) str() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) strands() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) structure() (rna_library.Motif method), [1] (rna_library.SecStruct property) (rna_library.structure.Motif method), [1] (rna_library.structure.motif.Motif method), [1] (rna_library.structure.SecStruct property) (rna_library.structure.secstruct.SecStruct property) symmetric() (rna_library.Junction method) (rna_library.structure.Junction method) (rna_library.structure.junction.Junction method)

T

to_str() (rna_library.BasePair method) (rna_library.core.BasePair method) (rna_library.core.enums.BasePair method) (rna_library.core.enums.Nucleotide method) (rna_library.core.Nucleotide method) (rna_library.Nucleotide method) token() (rna_library.Motif method), [1] (rna_library.structure.Motif method), [1] (rna_library.structure.motif.Motif method), [1]

type() (rna_library.Motif method) (rna_library.structure.Motif method) (rna_library.structure.motif.Motif method) TYPE_MAPPER (in module rna_library) (in module rna_library.core) (in module rna_library.core.enums)

U

U (rna_library.core.enums.Nucleotide attribute) (rna_library.core.Nucleotide attribute) (rna_library.Nucleotide attribute) UA (rna_library.BasePair attribute) (rna_library.core.BasePair attribute) (rna_library.core.enums.BasePair attribute)

UG (rna_library.BasePair attribute) (rna_library.core.BasePair attribute) (rna_library.core.enums.BasePair attribute) UNASSIGNED (rna_library.core.enums.MotifType attribute) (rna_library.core.MotifType attribute) (rna_library.MotifType attribute)

V

valid_db() (in module rna_library.core) (in module rna_library.core.util) validate_arguments_() (rna_library.JunctionEntry method) (rna_library.processing.junction_data.JunctionEntry method) (rna_library.processing.JunctionEntry method)

validate_barcode_constraints() (in module rna_library.design.barcode)