rna_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

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

`DF_VARS`
`IDX_NAME`
`ZARR_GROUP`
`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