rna_majiq.SpliceGraph

class rna_majiq.SpliceGraph(sg)

Representation of all possible splicing changes in each gene.

Representation of splicing in each gene as exons connected by spliced junctions and retained introns. This representation is composed of:

• the collection of all Contigs (e.g. chromosomes) on which genes can be defined (SpliceGraph.contigs),

• the collection of all Genes and their coordinates on the splicegraph contigs (SpliceGraph.genes),

• the collection of all Exons for each gene (SpliceGraph.exons),

• the collection of all GeneIntrons for each gene (SpliceGraph.introns),

• the collection of all GeneJunctions for each gene (SpliceGraph.junctions),

• ExonConnections associating introns and junctions to source and target exons, enabling the identification of splicing events, e.g. LSVs (SpliceGraph.exon_connections).

Parameters:

sg (rna_majiq.internals.SpliceGraph) – Underlying object binding the internal C++ API

See also

SpliceGraph.from_gff3

Initialize SpliceGraph from GFF3 file

SpliceGraph.from_components

Construct SpliceGraph from components

SpliceGraph.from_zarr

Load SpliceGraph saved in Zarr format

__init__(sg)

Construct SpliceGraph using object from internal C++ API

Parameters:

sg (rna_majiq.internals.SpliceGraph) – Underlying object binding the internal C++ API

Methods

__init__(sg)	Construct SpliceGraph using object from internal C++ API
combine(make_annotated, keep_denovo[, ...])	Combine input splicegraphs into single SpliceGraph.
from_components(contigs, genes, exons, ...)	Construct SpliceGraph with given components
from_gff3(path[, process_ir, gff3_types, ...])	Create SpliceGraph from GFF3 transcriptome annotations
from_zarr(store[, genes, preload])	Load SpliceGraph from specified path/store
get_gene_view([gene_idx, gene_id, gene_name])	Get view into specific gene (requires matplotlib)
modules([sg_mask])	Create GeneModules over this splicegraph with mask
to_sqlite(path[, genome_name])	Save splicegraph to legacy format
to_zarr(store[, mode])	Save SpliceGraph to specified path/store
with_updated_exon_connections(exon_connections)	Create SpliceGraph from exon connections with same genes

Attributes

contigs	The collection of all Contigs on which genes can be defined
exon_connections	ExonConnections for the splicegraph
exons	The collection of all Exons for each gene
genes	The collection of all Genes and their coordinates on contigs
introns	The collection of all GeneIntrons for each gene
junctions	The collection of all GeneJunctions for each gene
transcripts	The collection of all Genes and their coordinates on contigs