Likelihood Module
model_binomial
Section titled “model_binomial”def model_binomial(folder_in, in_file, chrom, file_out, file_no=None)Create binomial likelihood model first column - likelihood of background second column - likelihood of coverage
ChromosomeModel
Section titled “ChromosomeModel”class ChromosomeModel(folder, chrom)Args: folder: file with the model chrom: of which chromosome is the model
Attributes
Section titled “Attributes”Methods
Section titled “Methods”make_model
Section titled “make_model”def make_model(coverage_folder, coverage_prefix, file_no)Make a lh model of given chromosome from coverage files
Args: coverage_folder: path to name with coverage files coverage_prefix: prefixed used for making coverage files file_no: number of files from which model is being created
def read()Read model.
read_track
Section titled “read_track”def read_track(track)Read specific track from model.
ModelLH
Section titled “ModelLH”class ModelLH(file)Likelihood model class
Args: file: file containing the model
Attributes
Section titled “Attributes”Methods
Section titled “Methods”def make(coverage_folder, coverage_prefix, file_no, force=False)Make lh model for all chromosomes
Args: coverage_folder: folder with coverage files coverage_prefix: prefixed used for making coverage files file_no: number of file from which model is being made force: if overwrite an existing model
read_chrom
Section titled “read_chrom”def read_chrom(chrom)Read into model specific chromosome.
read_chrom_track
Section titled “read_chrom_track”def read_chrom_track(chrom, track)Read into model specific track for chromosome.
clear_chrom
Section titled “clear_chrom”def clear_chrom(chrom)Clear model for given chromosome.
def main(model_file, coverage_folder, coverage_prefix, file_no=None, force=False)Crate likelihood models for all chromosomes
Args: model_file: output name coverage_folder: folder with coverage files coverage_prefix: prefix used for making coverage files file_no: number of files used for making coverage tracks