CpG Module Documentation

Set of discriminant functions that can recognize structural and compositional features such as CpG islands, promoter regions and first splice-donor sites. Davuluri RV, Grosse I, Zhang MQ: Computational identification of promoters and first exons in the human genome. Nat Genet. 2001, 29(4):412-417. [PMID: 11726928]

ensembl.tools.anno.simple_feature_annotation.cpg.run_cpg(genome_file: PathLike, output_dir: Path, cpg_bin: Path = PosixPath('cpg_lh'), cpg_min_length: int = 400, cpg_min_gc_content: int = 50, cpg_min_oe: float = 0.6, num_threads: int = 1) → None

Run CpG islands on genomic slices

param genome_file:

Genome file path.

type genome_file:

PathLike

param output_dir:

Working directory path

type output_dir:

Path

param cpg_bin:

CpG software path.

type cpg_bin:

Path

param cpg_min_length:

Min length of CpG islands

type cpg_min_length:

int

param cpg_min_gc_content:

Min GC frequency percentage

type cpg_min_gc_content:

int

param cpg_min_oe:

Min ratio of the observed to expected number of CpG (CpGo/e)

type cpg_min_oe:

float

param num_threads:

int, number of threads.

type num_threads:

int

return:

None

rtype:

None