def regions_complement(regions):
comp_regions = encode.regions()
for region_name in regions.keys():
# store an alias for the region with name region_name - just readability
data = regions[region_name]
comp_regions[region_name] = encode.feature_region( data.length, (), region_name )
# for each feature interval, store the non-region *before* it
prev_end = -1
for fi in data.iter_feature_regions():
if fi.start - prev_end > 1:
comp_regions[region_name].add(interval(prev_end+1, fi.start-1))
prev_end = fi.end
# store the non-feature interval after the last feature interval
if prev_end < data.length - 1:
comp_regions[region_name].add(interval(prev_end+1, data.length-1))
return comp_regions
if verbose:
print >> output, "Region files parsed."
# close all of the open files
for fp in split_files:
fp.close()
lengths_file.close()
if verbose:
import time
startTime = time.time()
import encode
baseRegions = []
for i in xrange(len(regions_s_to_split)):
test = encode.regions()
baseRegions.append(test)
# for each named region in
for key in regions_s_to_split[0].keys():
# store the region boundaries for each area
region_boundaries = []
# a list of region's for this key
region_list = [ regions[key] for regions in regions_s_to_split ]
# make sure all of the lengths are the same
assert len(set( region.length for region in region_list )) == 1
# for each regions in the regions
# note that we require the regions 'line up'