new_majiq.SJExperiment

class rna_majiq.SJExperiment(introns, junctions)

Spliced junction and retained intron coverage for the same experiment.

Junctions and retained introns are defined over contigs, not genes (i.e. ContigIntrons, ContigJunctions, not GeneIntrons, GeneJunctions). Coverage assigned to these regions is later mapped to their gene equivalents (matching contig and strand; matching coordinates for junctions, matching annotated status and overlapping coordinates for introns).

Coverage is obtained over unique bins. Bins represent positions at which the start of the feature would intersect the aligned read. In the case of junctions, there is a single bin for each possible position, so the total number of bins/positions is determined by the maximum read length. For introns, nonzero length increases the total number of possible positions. In order to treat introns and junctions similarly, MAJIQ groups together contiguous positions into the same number of bins as junctions.

This is represented by:

SJIntronsBins with intron coverage and assigned regions (SJExperiment.introns),
SJJunctionsBins with junction coverage and assigned regions (SJExperiment.junctions).

Parameters:

introns (rna_majiq.SJIntronsBins)
junctions (rna_majiq.SJJunctionsBins)

See also

SJExperiment.from_bam: Load SJExperiment from BAM file
SJExperiment.from_zarr: Load SJExperiment saved to Zarr file

__init__(introns, junctions)

Initialize SJExperiment with intron and junction coverage

Parameters:

introns (rna_majiq.SJIntronsBins)
junctions (rna_majiq.SJJunctionsBins)

Notes

Enforces requirement that introns and junctions share the same original (bam) path and version of majiq used to do parsing

Methods

`__init__`(introns, junctions)	Initialize `SJExperiment` with intron and junction coverage
`detect_strand`(sj_junctions, sg[, minreads, ...])	Return `SJJunctionsBins` with appropriate strandness
`from_SJJunctionsBins`(junctions)	Return `SJExperiment` with junction coverage, no introns
`from_bam`(path, sg[, strandness, nthreads, ...])	Load `SJExperiment` from BAM file
`from_zarr`(store)	Load `SJExperiment` from specified path
`to_zarr`(store[, mode, consolidated])	Save `SJExperiment` to specified path/store

Attributes

`introns`	`SJIntronsBins` with intron coverage for this experiment
`junctions`	`SJJunctionsBins` with junctioncoverage for this experiment
`original_path`	Path to BAM file that was processed for coverage
`original_version`	Version of MAJIQ that was used to process the coverage