rna_majiq.Exons

class rna_majiq.Exons(exons)

Collection of exons per gene and their annotated/updated coordinates

__init__(exons)

Methods

__init__(exons)
checksum()
empty_introns()	Return empty GeneIntrons that match these exons
from_arrays(genes, gene_idx, start, end[, ...])	Create Exons from Genes and input arrays
from_zarr(store[, genes])	Read exons from zarr file/store
get_annotated()	Annotated Exons with original coordinates, excluding novel exons
index(gene_idx, start, end)	Get indexes of gene regions (-1 if not present)
infer_with_junctions(junctions[, full_inference])	Return updated Exons accommodating novel junctions per gene
is_denovo([exon_idx, annotated_exons])	Return denovo status of selected exons
is_exon_extension([exon_idx])	Return if exon(s) have exon extension
is_full_exon([exon_idx])	Return if exon(s) are full exons
is_half_exon([exon_idx])	Return if exon(s) are half exons
overlaps(other[, region_idx])	Get mask over region_idx indicating if they overlap regions in other
potential_introns([make_simplified])	GeneIntrons enumerating all possible introns between exons
slice_for_gene(gene_idx)
to_zarr(store, mode[, consolidated, drop_vars])	Serialize to zarr format.

Attributes

DF_VARS
IDX_NAME
ZARR_GROUP
annotated_end	Annotated coordinates end.
annotated_start	Annotated coordinates start.
df	xr.Dataset of specified data
end	End coordinate of each region
exon_idx
gene_idx	Index of gene on which region is defined
genes	Genes for which these regions are defined
start	Start coordinate of each region