tRNAscan-SE Module Documentation

tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25(5):955-64. [PMID: 9023104]

ensembl.tools.anno.snc_rna_annotation.trnascan.run_trnascan(genome_file: PathLike, output_dir: Path, trnascan_bin: Path = PosixPath('tRNAscan-SE'), trnascan_filter: Path = PosixPath('EukHighConfidenceFilter'), num_threads: int = 1) → None

Executes tRNAscan-SE on genomic slices

param genome_file:

Genome file path.

type genome_file:

PathLike

param output_dir:

working directory path.

type output_dir:

Path

param trnascan_bin:

tRNAscan-SE software path.

type trnascan_bin:

Path, default tRNAscan-SE

param trnascan_filter:

tRNAscan-SE filter set path.

type trnascan_filter:

Path, default EukHighConfidenceFilter

param num_threads:

int, number of threads.

type num_threads:

int, default 1

return:

None

rtype:

None