Index

A

all_constraints_pass() (dnachisel.CircularDnaOptimizationProblem method) all_variants() (dnachisel.DnaNotationPattern method) (dnachisel.MutationSpace.MutationSpace method) AllowPrimer (class in dnachisel.builtin_specifications) annotate_differences() (in module dnachisel.biotools) annotate_pattern_occurrences() (in module dnachisel.biotools) annotate_record() (in module dnachisel.biotools) apply_pseudocounts() (dnachisel.MotifPssmPattern class method)

apply_random_mutations() (dnachisel.MutationSpace.MutationSpace method) as_passive_objective() (dnachisel.Specification method) AvoidBlastMatches (class in dnachisel.builtin_specifications) AvoidChanges (class in dnachisel.builtin_specifications) AvoidHairpins (class in dnachisel.builtin_specifications) AvoidMatches (class in dnachisel.builtin_specifications) AvoidPattern (class in dnachisel.builtin_specifications) AvoidRareCodons (class in dnachisel.builtin_specifications) AvoidStopCodons (class in dnachisel.builtin_specifications)

B

blast_sequence() (in module dnachisel.biotools)

breach_label() (dnachisel.Specification method) breaches_records_to_pdf() (in module dnachisel.reports.constraints_reports)

C

change_biopython_record_sequence() (in module dnachisel.biotools) choices_span() (dnachisel.MutationSpace.MutationSpace property) CircularDnaOptimizationProblem (class in dnachisel) CodonOptimize() (in module dnachisel.builtin_specifications) complement() (in module dnachisel.biotools) compute_feature_box_linewidth() (dnachisel.reports.constraints_reports.GraphicTranslator static method)

compute_feature_color() (dnachisel.reports.constraints_reports.GraphicTranslator method) compute_feature_fontdict() (dnachisel.reports.constraints_reports.GraphicTranslator static method) compute_feature_label() (dnachisel.reports.constraints_reports.GraphicTranslator method) constrain_sequence() (dnachisel.MutationSpace.MutationSpace method) constraints_breaches_dataframe() (in module dnachisel.reports.constraints_reports) constraints_evaluations() (dnachisel.CircularDnaOptimizationProblem method) copy_with_changes() (dnachisel.Specification method)

D

default_message (in module dnachisel.SpecEvaluation) dict_to_pretty_string() (in module dnachisel.biotools) dna_pattern_to_regexpr() (in module dnachisel.biotools) dna_sequence_to_regexpr() (dnachisel.DnaNotationPattern static method) dnachisel.biotools module dnachisel.Location module dnachisel.MutationSpace module

dnachisel.reports.constraints_reports module dnachisel.reports.optimization_reports module dnachisel.SpecEvaluation module DnaNotationPattern (class in dnachisel) DnaOptimizationProblem (class in dnachisel)

E

EnforceGCContent (class in dnachisel.builtin_specifications) EnforceMeltingTemperature (class in dnachisel.builtin_specifications) EnforcePatternOccurence (class in dnachisel.builtin_specifications) EnforceRegionsCompatibility (class in dnachisel.builtin_specifications) EnforceSequence (class in dnachisel.builtin_specifications)

EnforceTranslation (class in dnachisel.builtin_specifications) EnzymeSitePattern (class in dnachisel) extended() (dnachisel.Location.Location method) extract_sequence() (dnachisel.Location.Location method) extract_varying_region() (dnachisel.MutationSpace.MutationChoice method)

F

find_all_bowtie_matches() (in module dnachisel.biotools) find_matches() (dnachisel.SequencePattern method) find_matches_in_string() (dnachisel.MotifPssmPattern method) find_specification_label_in_feature() (in module dnachisel.biotools)

from_biopython_location() (dnachisel.Location.Location static method) from_data() (dnachisel.Location.Location static method) from_optimization_problem() (dnachisel.MutationSpace.MutationSpace static method) from_sequences() (dnachisel.MotifPssmPattern class method) from_string() (dnachisel.EnzymeSitePattern static method)

G

gc_content() (in module dnachisel.biotools) GraphicTranslator (class in dnachisel.reports.constraints_reports)

group_nearby_indices() (in module dnachisel.biotools) group_nearby_segments() (in module dnachisel.biotools)

H

HarmonizeRCA (class in dnachisel.builtin_specifications)

HomopolymerPattern (class in dnachisel)

I

initialize() (dnachisel.DnaOptimizationProblem method)

initialized_on_problem() (dnachisel.Specification method)

L

label() (dnachisel.Specification method) label_parameters() (dnachisel.Specification method) list_common_enzymes() (in module dnachisel.biotools) list_from_file() (dnachisel.MotifPssmPattern class method)

load_record() (in module dnachisel.biotools) localized() (dnachisel.MutationSpace.MutationSpace method) (dnachisel.Specification method) Location (class in dnachisel.Location)

M

MatchTargetCodonUsage (class in dnachisel.builtin_specifications) MaximizeCAI (class in dnachisel.builtin_specifications) merge_overlapping_locations() (dnachisel.Location.Location static method) merge_with() (dnachisel.MutationSpace.MutationChoice method) module dnachisel.biotools dnachisel.Location dnachisel.MutationSpace dnachisel.reports.constraints_reports dnachisel.reports.optimization_reports dnachisel.SpecEvaluation

MotifPssmPattern (class in dnachisel) MutationChoice (class in dnachisel.MutationSpace) MutationSpace (class in dnachisel.MutationSpace)

N

number_of_edits() (dnachisel.DnaOptimizationProblem method)

O

objectives_evaluations() (dnachisel.CircularDnaOptimizationProblem method) optimize() (dnachisel.CircularDnaOptimizationProblem method)

optimize_with_report() (dnachisel.CircularDnaOptimizationProblem method) (dnachisel.DnaOptimizationProblem method) overlap_region() (dnachisel.Location.Location method)

P

pick_random_mutations() (dnachisel.MutationSpace.MutationSpace method)

R

random_dna_sequence() (in module dnachisel.biotools) random_protein_sequence() (in module dnachisel.biotools) random_variant() (dnachisel.MutationSpace.MutationChoice method) records_from_breaches_dataframe() (in module dnachisel.reports.constraints_reports) RepeatedKmerPattern (class in dnachisel)

resolve_constraints() (dnachisel.CircularDnaOptimizationProblem method) restrict_nucleotides() (dnachisel.Specification method) reverse_complement() (in module dnachisel.biotools) reverse_translate() (in module dnachisel.biotools) round_all_numbers_in_dict() (in module dnachisel.biotools)

S

score_to_formatted_string() (in module dnachisel.biotools) sequence_edits_as_array() (dnachisel.DnaOptimizationProblem method) sequence_to_biopython_record() (in module dnachisel.biotools) SequenceLengthBounds (class in dnachisel.builtin_specifications) SequencePattern (class in dnachisel) sequences_differences() (in module dnachisel.biotools) sequences_differences_array() (in module dnachisel.biotools)

sequences_differences_segments() (in module dnachisel.biotools) shifted() (dnachisel.Specification method) short_label() (dnachisel.Specification method) space_size() (dnachisel.MutationSpace.MutationSpace property) Specification (class in dnachisel) string_representation() (dnachisel.MutationSpace.MutationSpace method) subdivide_window() (in module dnachisel.biotools)

T

to_biopython_feature() (dnachisel.Location.Location method) to_biopython_location() (dnachisel.Location.Location method)

to_tuple() (dnachisel.Location.Location method) translate() (in module dnachisel.biotools)

U

UniquifyAllKmers (class in dnachisel.builtin_specifications)

W

windows_overlap() (in module dnachisel.biotools) write_no_solution_report() (in module dnachisel.reports.optimization_reports)

write_optimization_report() (in module dnachisel.reports.optimization_reports) write_record() (in module dnachisel.biotools)