Trf#
Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
API#
Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. .. rubric:: References
[2]
- ensembl.tools.anno.repeat_annotation.trf.run_trf(genome_file, output_dir, num_threads=1, trf_bin=PosixPath('trf'), match_score=2, mismatch_score=5, delta=7, pm=80, pi=10, minscore=40, maxperiod=500, bedtools_bin='/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/bin/bedtools')[source]#
- 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
- param bedtools_path:
Bedtools executable path.
- type bedtools_path:
str, default “/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/bin/bedtools”#pylint:disable=line-too-long
- return:
None
- rtype:
None