DENOFO models and choices

We provide a set of models and predefined choices which build our DENOFO annotation format. The heart of the format is the denofo.models.DeNovoGeneAnnotation

Models

class denofo.models.AnnotGenome(*, annotGenomeChoice: list[~denofo.choices.AnnotGenomeChoices] = <factory>)

annotGenomeChoice: list[AnnotGenomeChoices]

classmethod annotGenomeChoice_unknown(annotGenomeChoice: list[AnnotGenomeChoices], info: ValidationInfo) → list[AnnotGenomeChoices]

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class denofo.models.DeNovoGeneAnnotation(*, inputData: list[~denofo.choices.InputDataChoices] = <factory>, inputAnnotGenome: ~denofo.models.AnnotGenome | None = None, inputTranscriptome: ~denofo.models.Transcriptome | None = None, customInputData: str | None = None, evolutionaryInformation: ~denofo.models.EvolutionaryInformation | None = None, homologyFilter: ~denofo.models.HomologyFilter | None = None, nonCodingHomologs: ~denofo.models.NonCodingHomologs | None = None, translationalEvidence: ~denofo.models.TranslationalEvidence | None = None, studyURL: list[str] | None = None)

customInputData: str | None

evolutionaryInformation: EvolutionaryInformation | None

homologyFilter: HomologyFilter | None

inputAnnotGenome: AnnotGenome | None

inputData: list[InputDataChoices]

inputDataType_required() → Self

inputTranscriptome: Transcriptome | None

model_config: ClassVar[ConfigDict] = {'exclude_none': True, 'extra': 'forbid', 'title': 'De Novo Gene Annotation'}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

nonCodingHomologs: NonCodingHomologs | None

studyURL: list[str] | None

translationalEvidence: TranslationalEvidence | None

class denofo.models.EvolutionaryInformation(*, selection: str | None = None)

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

selection: str | None

class denofo.models.HomologyFilter(*, phylogeneticTaxa: ~denofo.models.PhylogeneticTaxa | None = None, seqType: list[~denofo.choices.SeqTypeChoices] = <factory>, customSeqType: list[str] | None = None, structuralSimilarity: str | None = None, threshold: list[~denofo.choices.ThresholdChoices] = <factory>, customThreshold: list[str] | None = None, thresholdValue: list[float] = <factory>, dataBase: list[~denofo.choices.HomologyDBChoices] = <factory>, customDB: list[str] | None = None)

customDB: list[str] | None

customSeqType: list[str] | None

customThreshold: list[str] | None

customs_required() → Self

dataBase: list[HomologyDBChoices]

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

phylogeneticTaxa: PhylogeneticTaxa | None

seqType: list[SeqTypeChoices]

structuralSimilarity: str | None

threshold: list[ThresholdChoices]

thresholdValue: list[float]

exception denofo.models.ModelValidError

Error raised when a model validation fails. Necessary to ignore field validators when checking only field validators.

class denofo.models.NonCodingHomologs(*, enablingMutations: bool = False, synteny: SyntenySearch | None = None)

enablingMutations: bool

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

synteny: SyntenySearch | None

class denofo.models.PhylogeneticTaxa(*, taxSpecificity: TaxSpecificityChoices = TaxSpecificityChoices.lineageSpecif, taxonID: TaxonID = TaxonID(taxID=''))

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

taxSpecificity: TaxSpecificityChoices

taxonID: TaxonID

class denofo.models.SyntenySearch(*, anchors: list[~denofo.choices.AnchorChoices] = <factory>, customAnchor: list[str] | None = None, softwareSyntenySearch: list[str] | None = None)

anchors: list[AnchorChoices]

customAnchor: list[str] | None

customAnchor_required() → Self

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

softwareSyntenySearch: list[str] | None

exception denofo.models.TaxIDTranslation

Warning raised when a taxon ID is translated to a taxon name or vice versa.

class denofo.models.TaxonID(*, taxID: str | int = '')

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

taxID: str | int

classmethod taxID_valid(taxID: str | int, info: ValidationInfo) → str | int

class denofo.models.Transcriptome(*, expressionLevel: float | None = None, transContextChoice: list[~denofo.choices.GeneticContextChoices] = <factory>, customGeneticContext: list[str] | None = None, transORFChoice: list[~denofo.choices.ORFChoices] = <factory>, customORF: list[str] | None = None, transcriptomeInfo: str | None = None)

customGeneticContext: list[str] | None

customGeneticContext_required() → Self

customORF: list[str] | None

customORFChoice_required() → Self

expressionLevel: float | None

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

transContextChoice: list[GeneticContextChoices]

transORFChoice: list[ORFChoices]

classmethod transORFChoice_exclude(transORFChoice: list[ORFChoices], info: ValidationInfo) → list[ORFChoices]

transcriptomeInfo: str | None

class denofo.models.TranslationalEvidence(*, translationEvidence: list[TranslationEvidenceChoices] | None = None, customTranslationEvidence: list[str] | None = None)

customTranslationEvidence: list[str] | None

customTranslationEvidence_required() → Self

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

translationEvidence: list[TranslationEvidenceChoices] | None

Choices

class denofo.choices.AnchorChoices(*values)

CUSTOM = 'custom choice'

GENEANCHOR = 'gene anchors'

GENOMEALIGNMENT = 'genome alignment'

class denofo.choices.AnnotGenomeChoices(*values)

abInitio = 'ab initio approach'

homology = 'homology-based approach'

unknown = 'unknown'

class denofo.choices.DirectionChoices(*values)

ANY = 'any direction'

FORWARD = 'forward'

class denofo.choices.GeneticContextChoices(*values)

CUSTOM = 'custom choice'

antisense = 'antisense'

intergenic = 'intergenic'

intronic = 'intronic'

overlap_gene = 'overlap gene'

class denofo.choices.HomologyDBChoices(*values)

CUSTOM = 'custom choice'

ENA = 'ENA (by EMBL-EBI)'

ENSEMBL = 'Ensembl'

INTERPRO = 'InterPro'

NCBINR = 'NCBI NR'

REFSEQ = 'RefSeq'

SWISSPROT = 'UniProtKB/Swiss-Prot'

TrEMBL = 'UniProtKB/TrEMBL'

class denofo.choices.InputDataChoices(*values)

ANNOT_GENOME = 'annotated genome'

CUSTOM = 'custom choice'

TRANSCRIPTOME = 'transcriptome'

class denofo.choices.ORFChoices(*values)

CUSTOM = 'custom choice'

allORF = 'all ORF'

firstORF = 'start first ORF'

highestKoz = 'highest Kozac'

long_5_3_ORF = 'long 5` 3` ORF'

longestORF = 'longest ORF'

noORF = 'no ORF'

class denofo.choices.SeqTypeChoices(*values)

CUSTOM = 'custom choice'

DNA = 'DNA'

FRAME6 = '6-frame translation'

NCRNA = 'ncRNAs'

PROT_SEQS = 'protein sequences'

RNA = 'RNA'

TE = 'transposable elements'

class denofo.choices.TaxSpecificityChoices(*values)

conditSpecif = 'tissue/condition-specific'

lineageSpecif = 'lineage-specific'

speciesSpecif = 'species-specific'

class denofo.choices.ThresholdChoices(*values)

COVERAGE = 'coverage [%]'

CUSTOM = 'custom choice'

EVALUE = 'e-value'

class denofo.choices.TranslationEvidenceChoices(*values)

CUSTOM = 'custom choice'

MASS_SPEC = 'mass spectrometry'

PERIODICITY = 'periodicity'

RIBO_PROFIL = 'ribosome profiling'