new_majiq.GeneIntrons

class rna_majiq.GeneIntrons(gene_introns)

Collection of introns per gene and their coordinates, flags, and exons

Parameters:

gene_introns (_GeneIntrons) – Underlying object binding the internal C++ API

__init__(gene_introns)

Methods

__init__(gene_introns)
build_group()	Create GroupIntronsGenerator to update these introns in place
checksum()	Checksum including passed/simplified/connections status
checksum_nodata()	Checksum only considering gene_idx, start, and end
connect_exons(exons)	Connect regions to specified exons
dst_exon_idx([region_idx])
filter_passed([keep_annotated, discard_denovo])	Return GeneIntrons subset that all passed build filters
from_arrays(genes, gene_idx, start, end[, ...])	Create connections object from Genes and input arrays
from_genes(genes[, connected_exons])	Empty introns matched to specified genes
from_zarr(store[, genes])	Load connections from zarr file or store.
index(gene_idx, start, end)	Get indexes of gene regions (-1 if not present)
is_denovo([gi_idx, annotated_introns])	Return denovo status of selected introns
overlaps(other[, region_idx])	Get mask over region_idx indicating if they overlap regions in other
propagate_through_annotated([...])	Propagate introns to annotated exons, then back to current exons.
propagate_to_annotated([annotated_exons, ...])	Get GeneIntrons for annotated exons
slice_for_gene(gene_idx)
src_exon_idx([region_idx])
to_zarr(store, mode[, consolidated, drop_vars])	Serialize to zarr format.
update_flags_from(donor_introns)	Update flags using overlapping donor GeneIntrons

Attributes

connected_exons	exons the connections are associated with (or None otherwise)
denovo	Indicate if each connection is denovo or not
df	xr.Dataset of specified data
end	End coordinate of each region
end_exon_idx	Indicate exon_idx associated with end coordinate
gene_idx	Index of gene on which region is defined
genes	Genes for which these regions are defined
gi_idx
passed_build	Indicate if each connection passed build filters (reliable) or not
simplified	Indicate if each connection is simplified or not
start	Start coordinate of each region
start_exon_idx	Indicate exon_idx associated with start coordinate