Repeatmasker#
RepeatMasker is a program that screens DNA sequences for interspersed
API#
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
References
[3]
- ensembl.tools.anno.repeat_annotation.repeatmasker.run_repeatmasker(genome_file, output_dir, repeatmasker_bin=PosixPath('RepeatMasker'), library='', repeatmasker_engine='rmblast', species='', num_threads=1, bedtools_bin='/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/bin/bedtools')[source]#
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
- param bedtools_bin:
Bedtools executable path.
- type bedtools_bin:
str, default “/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/bin/bedtools”#pylint:disable=line-too-long
- return:
None
- rtype:
None