LICENCE.txt
MANIFEST.in
README.rst
pypi-readme.rst
pyproject.toml
dnachisel/Location.py
dnachisel/__init__.py
dnachisel/cli.py
dnachisel/version.py
dnachisel.egg-info/PKG-INFO
dnachisel.egg-info/SOURCES.txt
dnachisel.egg-info/dependency_links.txt
dnachisel.egg-info/entry_points.txt
dnachisel.egg-info/requires.txt
dnachisel.egg-info/top_level.txt
dnachisel/DnaOptimizationProblem/CircularDnaOptimizationProblem.py
dnachisel/DnaOptimizationProblem/DnaOptimizationProblem.py
dnachisel/DnaOptimizationProblem/NoSolutionError.py
dnachisel/DnaOptimizationProblem/__init__.py
dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py
dnachisel/DnaOptimizationProblem/mixins/ObjectivesMaximizerMixin.py
dnachisel/DnaOptimizationProblem/mixins/RecordRepresentationMixin.py
dnachisel/DnaOptimizationProblem/mixins/__init__.py
dnachisel/MutationSpace/MutationChoice.py
dnachisel/MutationSpace/MutationSpace.py
dnachisel/MutationSpace/__init__.py
dnachisel/SequencePattern/DnaNotationPattern.py
dnachisel/SequencePattern/EnzymeSitePattern.py
dnachisel/SequencePattern/HomopolymerPattern.py
dnachisel/SequencePattern/MotifPssmPattern.py
dnachisel/SequencePattern/RepeatedKmerPattern.py
dnachisel/SequencePattern/SequencePattern.py
dnachisel/SequencePattern/__init__.py
dnachisel/Specification/FeatureRepresentationMixin.py
dnachisel/Specification/Specification.py
dnachisel/Specification/SpecificationSet.py
dnachisel/Specification/__init__.py
dnachisel/Specification/SpecEvaluation/ProblemConstraintsEvaluations.py
dnachisel/Specification/SpecEvaluation/ProblemObjectivesEvaluations.py
dnachisel/Specification/SpecEvaluation/SpecEvaluation.py
dnachisel/Specification/SpecEvaluation/SpecEvaluations.py
dnachisel/Specification/SpecEvaluation/__init__.py
dnachisel/biotools/__init__.py
dnachisel/biotools/biotables.py
dnachisel/biotools/blast_sequence.py
dnachisel/biotools/bowtie.py
dnachisel/biotools/enzymes_operations.py
dnachisel/biotools/formatting_operations.py
dnachisel/biotools/gc_content.py
dnachisel/biotools/genbank_operations.py
dnachisel/biotools/indices_operations.py
dnachisel/biotools/random_sequences.py
dnachisel/biotools/sequences_differences.py
dnachisel/biotools/sequences_operations.py
dnachisel/biotools/data/README.md
dnachisel/biotools/data/complements.csv
dnachisel/biotools/data/iupac_notation.csv
dnachisel/biotools/data/nucleotide_to_regexpr.csv
dnachisel/builtin_specifications/AllowPrimer.py
dnachisel/builtin_specifications/AvoidBlastMatches.py
dnachisel/builtin_specifications/AvoidChanges.py
dnachisel/builtin_specifications/AvoidHairpins.py
dnachisel/builtin_specifications/AvoidHeterodimerization.py
dnachisel/builtin_specifications/AvoidMatches.py
dnachisel/builtin_specifications/AvoidPattern.py
dnachisel/builtin_specifications/AvoidStopCodons.py
dnachisel/builtin_specifications/CodonSpecification.py
dnachisel/builtin_specifications/EnforceChanges.py
dnachisel/builtin_specifications/EnforceChoice.py
dnachisel/builtin_specifications/EnforceGCContent.py
dnachisel/builtin_specifications/EnforceMeltingTemperature.py
dnachisel/builtin_specifications/EnforcePatternOccurence.py
dnachisel/builtin_specifications/EnforceRegionsCompatibility.py
dnachisel/builtin_specifications/EnforceSequence.py
dnachisel/builtin_specifications/EnforceTerminalGCContent.py
dnachisel/builtin_specifications/EnforceTranslation.py
dnachisel/builtin_specifications/SequenceLengthBounds.py
dnachisel/builtin_specifications/TerminalSpecification.py
dnachisel/builtin_specifications/UniquifyAllKmers.py
dnachisel/builtin_specifications/__init__.py
dnachisel/builtin_specifications/codon_optimization/AvoidRareCodons.py
dnachisel/builtin_specifications/codon_optimization/BaseCodonOptimizationClass.py
dnachisel/builtin_specifications/codon_optimization/CodonOptimize.py
dnachisel/builtin_specifications/codon_optimization/HarmonizeRCA.py
dnachisel/builtin_specifications/codon_optimization/MatchTargetCodonUsage.py
dnachisel/builtin_specifications/codon_optimization/MaximizeCAI.py
dnachisel/builtin_specifications/codon_optimization/__init__.py
dnachisel/reports/SpecAnnotationsTranslator.py
dnachisel/reports/__init__.py
dnachisel/reports/colors_cycle.py
dnachisel/reports/optimization_reports.py
dnachisel/reports/tools.py
dnachisel/reports/assets/logo.png
dnachisel/reports/assets/optimization_report.pug
dnachisel/reports/assets/style.css
dnachisel/reports/constraints_reports/GraphicTranslator.py
dnachisel/reports/constraints_reports/__init__.py
dnachisel/reports/constraints_reports/constraints_breaches_dataframe.py
dnachisel/reports/constraints_reports/constraints_reports.py
dnachisel/utils/__init__.py
dnachisel/utils/utils.py
docs/.gitignore
docs/Makefile
docs/README.md
docs/build_and_deploy.sh
docs/conf.py
docs/examples.rst
docs/favicon.png
docs/index.rst
docs/make.bat
docs/makehtml.sh
docs/notes.rst
docs/requirements.txt
docs/_static/css/custom.css
docs/_static/images/confectionary.png
docs/_static/images/dnachisel_algorithm.gif
docs/_static/images/example_sequence.png
docs/_static/images/geometry2.png
docs/_static/images/html_logo.png
docs/_static/images/old_html_logo.png
docs/_static/images/pw_maze_black (copy).png
docs/_static/images/pw_maze_black.png
docs/_static/images/pw_maze_dark.png
docs/_static/images/pw_maze_white.png
docs/_static/images/report_screenshot.png
docs/_static/images/title.png
docs/_static/images/genbank_annotations/README.md
docs/_static/images/genbank_annotations/all_unique_kmers.png
docs/_static/images/genbank_annotations/all_unique_kmers_here.png
docs/_static/images/genbank_annotations/allow_primer.png
docs/_static/images/genbank_annotations/avoid_blast.png
docs/_static/images/genbank_annotations/avoid_matches.png
docs/_static/images/genbank_annotations/avoid_matches_mismatches.png
docs/_static/images/genbank_annotations/avoid_non_unique_segments.png
docs/_static/images/genbank_annotations/avoid_pattern_cg.png
docs/_static/images/genbank_annotations/avoid_pattern_cg_obj.png
docs/_static/images/genbank_annotations/avoid_pattern_enzyme.png
docs/_static/images/genbank_annotations/avoid_pattern_kmer.png
docs/_static/images/genbank_annotations/avoid_pattern_noisoleucine.png
docs/_static/images/genbank_annotations/avoid_pattern_regex.png
docs/_static/images/genbank_annotations/boosting.png
docs/_static/images/genbank_annotations/cds.png
docs/_static/images/genbank_annotations/cds_enforce.png
docs/_static/images/genbank_annotations/change.png
docs/_static/images/genbank_annotations/change_objective.png
docs/_static/images/genbank_annotations/choice.png
docs/_static/images/genbank_annotations/codon_optimize.png
docs/_static/images/genbank_annotations/enforce_melting.png
docs/_static/images/genbank_annotations/enforce_melting_and_kmers.png
docs/_static/images/genbank_annotations/enforce_melting_obj.png
docs/_static/images/genbank_annotations/enforce_sequence.png
docs/_static/images/genbank_annotations/examples.csv
docs/_static/images/genbank_annotations/gc_range.png
docs/_static/images/genbank_annotations/gc_target.png
docs/_static/images/genbank_annotations/generate_annotations.py
docs/_static/images/genbank_annotations/harmonize_rca.png
docs/_static/images/genbank_annotations/insert.png
docs/_static/images/genbank_annotations/insert_several.png
docs/_static/images/genbank_annotations/keep.png
docs/_static/images/genbank_annotations/keep_obj.png
docs/_static/images/genbank_annotations/match_codon_usage.png
docs/_static/images/genbank_annotations/multiple_specs.png
docs/_static/images/genbank_annotations/myspec.png
docs/_static/images/genbank_annotations/use_best_codon.png
docs/genbank/genbank_api.rst
docs/genbank/genbank_notes.rst
docs/ref/biotools.rst
docs/ref/builtin_specifications.rst
docs/ref/cli.rst
docs/ref/constraints_reports.rst
docs/ref/core_classes.rst
docs/ref/reports.rst
examples/builtin_specifications_examples/example_AvoidBlastMatches.py
examples/builtin_specifications_examples/example_AvoidChanges_as_objective.py
examples/builtin_specifications_examples/example_AvoidHairpins.py
examples/builtin_specifications_examples/example_AvoidMatches.py
examples/builtin_specifications_examples/example_AvoidPattern.py
examples/builtin_specifications_examples/example_CodonOptimize.py
examples/builtin_specifications_examples/example_CodonOptimize_as_constraint.py
examples/builtin_specifications_examples/example_EnforcePattern.py
examples/builtin_specifications_examples/example_EnforceRegionsCompatibility.py
examples/builtin_specifications_examples/example_custom_specification.py
examples/builtin_specifications_examples/example_gene_PCR-tagging.py
examples/builtin_specifications_examples/example_max_random_iters.py
examples/common_scenarios/circular_sequence.py
examples/common_scenarios/ecoli_genes_optimization.py
examples/common_scenarios/gen9_9mer_score_minimization.py
examples/common_scenarios/gene_domestication.py
examples/common_scenarios/genome-wide-optimization.py
examples/common_scenarios/optimization_with_report.py
examples/common_scenarios/plasmid_optimization.py
examples/common_scenarios/primers_collection.py
examples/common_scenarios/sequence_without_restriction_sites.py
examples/common_scenarios/sequence_without_tf_binding_sites.py
examples/common_scenarios/constraints_breaches_report/constraints_breaches_report.py
examples/manuscript_examples/C_sequence_without_sites.py
examples/manuscript_examples/D_genome-wide-optimization.py
examples/manuscript_examples/B_multiobjectives/competing_objectives_example.py
tests/test_Location.py
tests/test_MutationChoices.py
tests/test_NoSolutionError.py
tests/test_biotools.py
tests/test_circular_sequences.py
tests/test_constraints_reports.py
tests/test_features_annotations.py
tests/test_io.py
tests/test_optimization_with_report.py
tests/test_patterns.py
tests/test_utils.py
tests/builtin_specifications/test_AllowPrimer.py
tests/builtin_specifications/test_AvoidBlastMatches.py
tests/builtin_specifications/test_AvoidChanges.py
tests/builtin_specifications/test_AvoidHairpins.py
tests/builtin_specifications/test_AvoidMatches.py
tests/builtin_specifications/test_AvoidPattern.py
tests/builtin_specifications/test_AvoidRareCodons.py
tests/builtin_specifications/test_AvoidStopCodons.py
tests/builtin_specifications/test_CodonOptimize.py
tests/builtin_specifications/test_EnforceChanges.py
tests/builtin_specifications/test_EnforceChoice.py
tests/builtin_specifications/test_EnforceGCContent.py
tests/builtin_specifications/test_EnforceMeltingTemperature.py
tests/builtin_specifications/test_EnforcePatternOccurence.py
tests/builtin_specifications/test_EnforceRegionsCompatibility.py
tests/builtin_specifications/test_EnforceSequence.py
tests/builtin_specifications/test_EnforceTerminalGCContent.py
tests/builtin_specifications/test_EnforceTranslation.py
tests/builtin_specifications/test_SequenceLengthBounds.py
tests/builtin_specifications/test_UniquifyAllKmers.py
tests/test_determinism/test_determinism.py
tests/test_scenarios/test_primers_collection.py
tests/tests_from_genbanks/test_from_genbanks.py