Module epiclass.utils.write_chrom_filter

Create a custom bed filter for each chromosome, to select a fixed region on the second arm center.

Functions

def compute_second_arm_region(centromere_end, chromsize, width=30300000, resolution=100000)

Return a region of given width (begin,end) in the middle of the bigger chrom arm.

The given resolution fixes the position of the beginning to fit with the binning.

def load_centromeres(bed_filepath)

Return chrom_name:(centromere_begin, centromere_end) dict.

def load_chroms(chromsizes_filepath)

Return chrom_name:size dict.

def main()

Make a bed file for each chromosome with a fixed section of the second arm region.

def print_chr14_filter()

Print in bed format 303 regions of 100kb of chr14.