Data

Classes and utilities for manipulating genomics data.

Fold Intervals

data.fold_intervals.Subset(value)	Subset of the data.
data.fold_intervals.get_all_folds()	Returns the names of all data folds.
data.fold_intervals.get_fold_names(...)	Returns the data folds used for the model version.
data.fold_intervals.get_fold_intervals(...)	Returns the training intervals for the model version.

Genome

data.genome.Strand(value)	Represents the strand of a DNA sequence.
data.genome.Interval(chromosome, start, end)	Represents a genomic interval.
data.genome.Variant(chromosome, position, ...)	Represents a genomic variant/mutation.
data.genome.Junction(chromosome, start, end)	Represents a splice junction.

Gene annotation

data.gene_annotation.TranscriptType(value)	Valid Transcript types available in the GENCODE GTF.
data.gene_annotation.extract_tss(gtf[, feature])	Extract transcription start sites (TSS) from a DataFrame.
data.gene_annotation.filter_transcript_type(gtf)	Filter GTF entries by transcript types.
data.gene_annotation.filter_protein_coding(gtf)	Filter GTF entries to only protein-coding genes.
data.gene_annotation.filter_to_longest_transcript(gtf)	Filter GTF entries to only the longest transcript per gene.
data.gene_annotation.filter_transcript_support_level(...)	Filter GTF to only transcripts with specific GENCODE support levels.
data.gene_annotation.get_gene_interval(gtf)	Returns a stranded genome.Interval given a gene identifier.
data.gene_annotation.get_gene_intervals(gtf)	Returns a list of stranded `genome.Interval`s for the given identifiers.

Junction data

data.junction_data.JunctionData(junctions, ...)	Container for storing splice junction data.
data.junction_data.get_junctions_to_plot(*, ...)	Gets a list of junctions to plot.

Ontology

data.ontology.OntologyType(value)	Supported ontology types.
data.ontology.OntologyTerm(type, id)	A single biological ontology term.

Track data

data.track_data.TrackData(values, metadata)	Container for storing track values and metadata.
data.track_data.concat(track_datas[, ...])	Concatenates multiple TrackData objects along the track dimension.
data.track_data.interleave(track_datas, ...)	Interleaves multiple TrackData objects by alternating rows.

Transcript

data.transcript.Transcript(exons[, cds, ...])	Represents transcript object containing attributes from a GTF file.
data.transcript.TranscriptExtractor(gtf_df)	Transcript extractor from gtf.