Repeatmasker Module Documentation

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0

ensembl.tools.anno.repeat_annotation.repeatmasker.run_repeatmasker(genome_file: PathLike, output_dir: Path, repeatmasker_bin: Path = PosixPath('RepeatMasker'), library: str = '', repeatmasker_engine: str = 'rmblast', species: str = '', num_threads: int = 1) → None

Executes RepeatMasker on the genome slices and stores the final annotation.gtf in repeatmasker_output

param genome_file:

Genome file path.

type genome_file:

PathLike

param output_dir:

Output directory path.

type output_dir:

Path

param repeatmasker_bin:

RepeatMasker executable path.

type repeatmasker_bin:

Path, default RepeatMasker

param library:

Custom repeat library.

type library:

str

param repeatmasker_engine:

RepeatMasker engine.

type repeatmasker_engine:

str, default rmblast

param species:

Species name.

type species:

str

param num_threads:

Number of threads.

type num_threads:

int, default 1

return:

None

rtype:

None