rna_majiq.SpliceGraph.from_gff3

classmethod SpliceGraph.from_gff3(path, process_ir=True, gff3_types=None, log_function=None)

Create SpliceGraph from GFF3 transcriptome annotations

Parameters:

• path (Union[str, Path]) – Path to GFF3 file (can be gzipped)

• process_ir (bool) – Identify annotated introns. This should generally be True

• gff3_types (Optional[GFF3TypesMap]) – How GFF3 lines will be parsed hierarchically for genes, transcript, and exon definitions. If None, use default initialization of GFF3TypesMap.

• log_function (Optional[Callable[str, str, int]]) – GFF3 types that were not accepted or explicitly ignored will be reported per unique type/part of hierarchy where they were missing, along with their counts. This function will be called for each unique type: log_function(type, location_in_hierarchy, count).