seriesoftubes.bedgraph

seriesoftubes.bedgraph.in_window_factory(chrom, start, end)

function factory

returns a function that checks if a bedgraph line overlaps a given interval. along with UCSC convention, end coordinate is open and start coordinate is 0-based (also compatible with BED files)

seriesoftubes.bedgraph.in_windows_factory(intervals)

function factory

returns a function that checks if a bedgraph line overlaps any given interval. assumes we already filtered by chrom

intervals must be given as tuples (int start, int end)

along with UCSC convention, end coordinate is open and start coordinate is 0-based (also compatible with BED files)

seriesoftubes.bedgraph.window_to_iter(chrom, start, end, filename, my_type=<type 'int'>)

generator that returns the values in a region [start,end) on chrom

from a bedgraph file called filename

note: bedgraph values are assumed to be ints unless my_type is set to something else