Eponine Module Documentation

Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy. Down TA, Hubbard TJ. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 2002 Mar;12(3):458-61. doi: 10.1101/gr.216102. PMID: 11875034; PMCID: PMC155284.

ensembl.tools.anno.simple_feature_annotation.eponine.run_eponine(genome_file: PathLike, output_dir: Path, num_threads: int = 1, java_bin: Path = PosixPath('java'), eponine_bin: Path = PosixPath('/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/opt/eponine/libexec/eponine-scan.jar'), eponine_threshold: float = 0.999) → None

Run Eponine on genomic slices

param genome_file:

Genome file path.

param genome_file:

PathLike

param output_dir:

Working directory path.

param output_dir:

Path

param java_bin:

Java path.

param java_bin:

Path, default java

param eponine_bin:

Eponine software path

param eponine_bin:

Path

param num_threads:

Number of threads.

param num_threads:

int, default 1

return:

None

rtype:

None