Index

A

abInitio (denofo.choices.AnnotGenomeChoices attribute) add_extension() (in module denofo.utils.helpers) allORF (denofo.choices.ORFChoices attribute) AnchorChoices (class in denofo.choices) anchors (denofo.models.SyntenySearch attribute) ANNOT_GENOME (denofo.choices.InputDataChoices attribute) annotate_fasta() (in module denofo.converter.convert)

annotate_gff() (in module denofo.converter.convert) AnnotGenome (class in denofo.models) annotGenomeChoice (denofo.models.AnnotGenome attribute) annotGenomeChoice_unknown() (denofo.models.AnnotGenome class method) AnnotGenomeChoices (class in denofo.choices) antisense (denofo.choices.GeneticContextChoices attribute) ANY (denofo.choices.DirectionChoices attribute)

B

Back_button (class in denofo.questionnaire.questionnaire_gui)

C

call_last_question() (denofo.questionnaire.questions.DeNovoQuestionnaire method) call_next_question() (denofo.questionnaire.questions.DeNovoQuestionnaire method) check_NCBI_taxDB() (in module denofo.utils.ncbiTaxDBcheck) clearLayout() (in module denofo.questionnaire.questionnaire_gui) closeEvent() (denofo.comparator.comparator_gui.DNGFCompareGUI method) (denofo.converter.converter_gui.DngfConverterGUI method) (denofo.questionnaire.questionnaire_gui.MainWindow method) compare_two_models() (in module denofo.utils.helpers) conditSpecif (denofo.choices.TaxSpecificityChoices attribute) convert_to_json() (in module denofo.converter.convert) convert_to_pickle() (in module denofo.converter.convert) COVERAGE (denofo.choices.ThresholdChoices attribute) CUSTOM (denofo.choices.AnchorChoices attribute) (denofo.choices.GeneticContextChoices attribute) (denofo.choices.HomologyDBChoices attribute) (denofo.choices.InputDataChoices attribute) (denofo.choices.ORFChoices attribute) (denofo.choices.SeqTypeChoices attribute) (denofo.choices.ThresholdChoices attribute) (denofo.choices.TranslationEvidenceChoices attribute)

Custom_entry (class in denofo.questionnaire.questionnaire_gui) custom_entry_insertion() (in module denofo.questionnaire.questionnaire_cli) customAnchor (denofo.models.SyntenySearch attribute) customAnchor_required() (denofo.models.SyntenySearch method) customDB (denofo.models.HomologyFilter attribute) customGeneticContext (denofo.models.Transcriptome attribute) customGeneticContext_required() (denofo.models.Transcriptome method) customInputData (denofo.models.DeNovoGeneAnnotation attribute) customORF (denofo.models.Transcriptome attribute) customORFChoice_required() (denofo.models.Transcriptome method) customs_required() (denofo.models.HomologyFilter method) customSeqType (denofo.models.HomologyFilter attribute) customThreshold (denofo.models.HomologyFilter attribute) customTranslationEvidence (denofo.models.TranslationalEvidence attribute) customTranslationEvidence_required() (denofo.models.TranslationalEvidence method)

D

dataBase (denofo.models.HomologyFilter attribute) decode_short_str() (in module denofo.converter.convert) denofo.choices module denofo.comparator.comparator_cli module denofo.comparator.comparator_gui module denofo.comparator.compare module denofo.converter.convert module denofo.converter.converter_cli module denofo.converter.converter_gui module denofo.models module denofo.questionnaire.questionnaire_cli module

denofo.questionnaire.questionnaire_gui module denofo.questionnaire.questions module denofo.utils.constants module denofo.utils.helpers module denofo.utils.ncbiTaxDBcheck module DeNovoGeneAnnotation (class in denofo.models) DeNovoQuestionnaire (class in denofo.questionnaire.questions) diff_two_lists() (in module denofo.utils.helpers) different_answers() (in module denofo.utils.helpers) DirectionChoices (class in denofo.choices) DNA (denofo.choices.SeqTypeChoices attribute) DNGFCompareGUI (class in denofo.comparator.comparator_gui) DngfConverterGUI (class in denofo.converter.converter_gui)

E

ENA (denofo.choices.HomologyDBChoices attribute) enablingMutations (denofo.models.NonCodingHomologs attribute) encode_short_str() (in module denofo.converter.convert) ENSEMBL (denofo.choices.HomologyDBChoices attribute) Enum_choice_selection (class in denofo.questionnaire.questionnaire_gui)

enum_choice_selection() (in module denofo.questionnaire.questionnaire_cli) ErrorDialog (class in denofo.questionnaire.questionnaire_gui) EVALUE (denofo.choices.ThresholdChoices attribute) EvolutionaryInformation (class in denofo.models) evolutionaryInformation (denofo.models.DeNovoGeneAnnotation attribute) expressionLevel (denofo.models.Transcriptome attribute)

F

firstORF (denofo.choices.ORFChoices attribute)

FORWARD (denofo.choices.DirectionChoices attribute) FRAME6 (denofo.choices.SeqTypeChoices attribute)

G

GENEANCHOR (denofo.choices.AnchorChoices attribute) GeneticContextChoices (class in denofo.choices) GENOMEALIGNMENT (denofo.choices.AnchorChoices attribute) get_custom_entry() (in module denofo.questionnaire.questionnaire_cli) (in module denofo.questionnaire.questionnaire_gui) get_DeNovoGeneAnnotation_from_qstack() (denofo.questionnaire.questions.DeNovoQuestionnaire method) get_enum_choice_conversion() (in module denofo.questionnaire.questionnaire_cli) (in module denofo.questionnaire.questionnaire_gui)

get_model_from_qstack_dict() (in module denofo.utils.helpers) get_model_from_short_repr() (in module denofo.utils.helpers) get_short_repr() (in module denofo.utils.helpers) get_yes_no() (in module denofo.questionnaire.questionnaire_cli) (in module denofo.questionnaire.questionnaire_gui) GoQBack (class in denofo.utils.constants)

H

highestKoz (denofo.choices.ORFChoices attribute) homology (denofo.choices.AnnotGenomeChoices attribute)

HomologyDBChoices (class in denofo.choices) HomologyFilter (class in denofo.models) homologyFilter (denofo.models.DeNovoGeneAnnotation attribute)

I

infer_format_from_extension() (in module denofo.utils.helpers) init_colors() (in module denofo.questionnaire.questionnaire_cli) inputAnnotGenome (denofo.models.DeNovoGeneAnnotation attribute) inputData (denofo.models.DeNovoGeneAnnotation attribute) InputDataChoices (class in denofo.choices)

inputDataType_required() (denofo.models.DeNovoGeneAnnotation method) inputTranscriptome (denofo.models.DeNovoGeneAnnotation attribute) intergenic (denofo.choices.GeneticContextChoices attribute) INTERPRO (denofo.choices.HomologyDBChoices attribute) intronic (denofo.choices.GeneticContextChoices attribute)

L

lineageSpecif (denofo.choices.TaxSpecificityChoices attribute) load_from_fasta() (in module denofo.converter.convert) load_from_gff() (in module denofo.converter.convert)

load_from_json() (in module denofo.converter.convert) load_from_pickle() (in module denofo.converter.convert) long_5_3_ORF (denofo.choices.ORFChoices attribute) longestORF (denofo.choices.ORFChoices attribute)

M

main() (in module denofo.comparator.comparator_cli) (in module denofo.comparator.comparator_gui) (in module denofo.converter.converter_cli) (in module denofo.questionnaire.questionnaire_cli) (in module denofo.questionnaire.questionnaire_gui) main_app() (in module denofo.questionnaire.questionnaire_gui) MainWindow (class in denofo.questionnaire.questionnaire_gui) MASS_SPEC (denofo.choices.TranslationEvidenceChoices attribute) model_config (denofo.models.AnnotGenome attribute) (denofo.models.DeNovoGeneAnnotation attribute) (denofo.models.EvolutionaryInformation attribute) (denofo.models.HomologyFilter attribute) (denofo.models.NonCodingHomologs attribute) (denofo.models.PhylogeneticTaxa attribute) (denofo.models.SyntenySearch attribute) (denofo.models.TaxonID attribute) (denofo.models.Transcriptome attribute) (denofo.models.TranslationalEvidence attribute)

ModelValidError module denofo.choices denofo.comparator.comparator_cli denofo.comparator.comparator_gui denofo.comparator.compare denofo.converter.convert denofo.converter.converter_cli denofo.converter.converter_gui denofo.models denofo.questionnaire.questionnaire_cli denofo.questionnaire.questionnaire_gui denofo.questionnaire.questions denofo.utils.constants denofo.utils.helpers denofo.utils.ncbiTaxDBcheck

N

NCBINR (denofo.choices.HomologyDBChoices attribute) NCBITAXDBWarning NCRNA (denofo.choices.SeqTypeChoices attribute)

NonCodingHomologs (class in denofo.models) nonCodingHomologs (denofo.models.DeNovoGeneAnnotation attribute) noORF (denofo.choices.ORFChoices attribute)

O

ORFChoices (class in denofo.choices)

overlap_gene (denofo.choices.GeneticContextChoices attribute)

P

PERIODICITY (denofo.choices.TranslationEvidenceChoices attribute) PhylogeneticTaxa (class in denofo.models)

phylogeneticTaxa (denofo.models.HomologyFilter attribute) ProgressBar (class in denofo.questionnaire.questionnaire_gui) PROT_SEQS (denofo.choices.SeqTypeChoices attribute)

Q

q1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_2() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_2_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_2_2() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_2_3() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_2_4() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_2_5() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_2_6() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_2_7() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q1_3() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_2() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_2_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_3() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_4() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_5_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_5_2() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_5_3() (denofo.questionnaire.questions.DeNovoQuestionnaire method)

q2_6() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_6_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_7() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q2_8() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q3() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q3_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q3_2() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q3_3() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q3_3_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q3_3_2() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q3_3_3() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q4() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q4_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q5() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q5_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q5_2() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q6() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q6_1() (denofo.questionnaire.questions.DeNovoQuestionnaire method) q_end() (denofo.questionnaire.questions.DeNovoQuestionnaire method) QSingleton (class in denofo.questionnaire.questionnaire_gui)

R

REFSEQ (denofo.choices.HomologyDBChoices attribute)

RIBO_PROFIL (denofo.choices.TranslationEvidenceChoices attribute) RNA (denofo.choices.SeqTypeChoices attribute)

S

save_annotation() (in module denofo.questionnaire.questionnaire_gui) selection (denofo.models.EvolutionaryInformation attribute) seqType (denofo.models.HomologyFilter attribute) SeqTypeChoices (class in denofo.choices) show_error_message() (in module denofo.questionnaire.questionnaire_gui) softwareSyntenySearch (denofo.models.SyntenySearch attribute)

speciesSpecif (denofo.choices.TaxSpecificityChoices attribute) start_questionnaire() (denofo.questionnaire.questions.DeNovoQuestionnaire method) structuralSimilarity (denofo.models.HomologyFilter attribute) studyURL (denofo.models.DeNovoGeneAnnotation attribute) SWISSPROT (denofo.choices.HomologyDBChoices attribute) synteny (denofo.models.NonCodingHomologs attribute) SyntenySearch (class in denofo.models)

T

taxID (denofo.models.TaxonID attribute) taxID_valid() (denofo.models.TaxonID class method) TaxIDTranslation TaxonID (class in denofo.models) taxonID (denofo.models.PhylogeneticTaxa attribute) taxSpecificity (denofo.models.PhylogeneticTaxa attribute) TaxSpecificityChoices (class in denofo.choices) TE (denofo.choices.SeqTypeChoices attribute) threshold (denofo.models.HomologyFilter attribute) ThresholdChoices (class in denofo.choices) thresholdValue (denofo.models.HomologyFilter attribute)

transContextChoice (denofo.models.Transcriptome attribute) Transcriptome (class in denofo.models) TRANSCRIPTOME (denofo.choices.InputDataChoices attribute) transcriptomeInfo (denofo.models.Transcriptome attribute) TranslationalEvidence (class in denofo.models) translationalEvidence (denofo.models.DeNovoGeneAnnotation attribute) translationEvidence (denofo.models.TranslationalEvidence attribute) TranslationEvidenceChoices (class in denofo.choices) transORFChoice (denofo.models.Transcriptome attribute) transORFChoice_exclude() (denofo.models.Transcriptome class method) TrEMBL (denofo.choices.HomologyDBChoices attribute)

U

unknown (denofo.choices.AnnotGenomeChoices attribute)

update_NCBI_taxDB() (in module denofo.utils.ncbiTaxDBcheck)

V

valid_input_for_pydmodel() (in module denofo.questionnaire.questionnaire_cli) (in module denofo.questionnaire.questionnaire_gui)

W

write_comparison() (in module denofo.comparator.compare)

Y

Yes_no (class in denofo.questionnaire.questionnaire_gui)

yes_or_no() (in module denofo.questionnaire.questionnaire_cli)