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RegionSet

RegionSet is Python representation of a genomic region set, commonly named as BED file.

🧪 Quick example

from gtars.models import RegionSet

# Create a RegionSet from a BED file
rs = RegionSet("https://data2.bedbase.org/files/d/a/dafd661aa70590999e0ff9e1980217db.bed.gz")

# Get identifier for the RegionSet
rs.identifier

Main commands

  • Load a BED file from local path or URL 
    rs = RegionSet("path/to/bedfile.bed")
  • Get number of regions 
    len(rs)
  • Calculate mean reagion width 
    rs.mean_region_width()
  • Get last base pair location for each chromosome 
    rs.get_max_end_per_ch()
  • Get number of base pairs in the region set 
    rs.get_nucleotide_length()
  • Save the regionSet as a BED file 
    rs.to_bed("path/to/save/bedfile.bed")
rs.to_bed_gz("path/to/save/bedfile.bed.gz")  # gzipped
  • Save the regionSet as a bigBed file 
    rs.to_bigbed("path/to/save/bedfile.bb", chrom_sizes="path/to/chrom.sizes")