TRF Module Documentation

Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27(2):573–580. doi:10.1093/nar/27.2.573

ensembl.tools.anno.repeat_annotation.trf.run_trf(genome_file: PathLike, output_dir: Path, num_threads: int = 1, trf_bin: Path = PosixPath('trf'), match_score: int = 2, mismatch_score: int = 5, delta: int = 7, pm: int = 80, pi: int = 10, minscore: int = 40, maxperiod: int = 500) → None

Executes TRF on genomic slices

param genome_file:

Genome file path.

type genome_file:

PathLike

param output_dir:

Working directory path.

type output_dir:

Path

param num_threads:

int, number of threads.

type num_threads:

int, default 1

param trf_bin:

TRF software path.

type trf_bin:

Path, default trf

param match_score:

Matching weight.

type match_score:

int, default 2

param mismatch_score:

Mismatching penalty.

type mismatch_score:

int, default 5

param delta:

Indel penalty.

type delta:

int, default 7

param pm:

Match probability (whole number).

type pm:

int, default 80

param pi:

Indel probability (whole number).

type pi:

int, default 10

param minscore:

Minimum alignment score to report.

type minscore:

int, default 40

param maxperiod:

Maximum period size to report.

type maxperiod:

int, default 500

return:

None

rtype:

None