rna_majiq.SJJunctionsBins

class rna_majiq.SJJunctionsBins(sj_junctionsbins, strandness, original_path, original_version, original_time, prefix=None, **additional_metadata)

Per-bin read coverage over junctions

Parameters:

sj_intronsbins (_SJIntronsBins) – Underlying object binding the internal C++ API
strandness (ExperimentStrandness) – strandness that was used for the experiment
original_path (str) – Original path to BAM file from which coverage was derived
original_version, original_time (str) – Version of MAJIQ and time BAM file was processed

See also

SJExperiment.from_bam, SJJunctionsBins.from_bam, SJJunctionsBins.from_zarr

__init__(sj_junctionsbins, strandness, original_path, original_version, original_time, prefix=None, **additional_metadata)

Methods

`__init__`(sj_junctionsbins, strandness, ...)
`flip_strand`()	Flip +/- strand reads to -/+ strand reads
`from_arrays`(regions, bin_reads, bin_idx, ...)	Create `SJJunctionsBins` from `SJJunctions`, arrays, metadata
`from_bam`(path[, strandness, nthreads])	Load SJJunctionsBins from BAM file
`from_zarr`(store)	Load SJJunctionsBins from zarr format
`numbins`([region_idx, minreads])	Number of bins for regions with at least specified number of reads
`numreads`([region_idx, numstacks])	Calculate total number of reads at specified regions with stacks
`numstacks`([region_idx, pvalue_threshold])	Calculate number of stacks at specified regions/pvalues
`prefix_from_zarr`(store)	Extract prefix from zarr with SJJunctionsBins
`project_reads`(new_junctions, new_strandness)	Project reads from self onto matching junctions in new_junctions
`rename_prefix`(new_prefix)	Create updated self where self.prefix is set to new_prefix
`to_unstranded`()	Convert stranded junction reads to unstranded junctions
`to_zarr`(store[, mode, consolidated])	Serialize to zarr format
`with_summaries`(regions, numreads, numbins, ...)	Create `SJJunctionsBins` with uniform coverage over nonzero bins

Attributes

`IDX_NAME`
`bin_idx`	index of each bin on each region
`bin_reads`	number of reads for each region/bin
`bin_reads_2d`	2D array representation of reads per region/bin
`df`	View of read counts per bin (combined with underlying regions)
`original_path`
`original_time`
`original_version`
`prefix`	Experiment name associated with these bin reads.
`regions`
`sjb_idx`
`sjb_idx_end`
`sjb_idx_start`
`strandness`
`total_bins`	total possible number of bins (defined by positions for junctions)