def do_access(fa_fname, exclude_fnames=(), min_gap_size=5000):
"""List the locations of accessible sequence regions in a FASTA file."""
access_regions = GA.from_rows(get_regions(fa_fname))
for ex_fname in exclude_fnames:
excluded = tabio.read(ex_fname, 'bed3')
access_regions = access_regions.subtract(excluded)
return GA.from_rows(join_regions(access_regions, min_gap_size))
def do_access(fa_fname, exclude_fnames=(), min_gap_size=5000,
skip_noncanonical=True):
"""List the locations of accessible sequence regions in a FASTA file."""
fa_regions = get_regions(fa_fname)
if skip_noncanonical:
fa_regions = drop_noncanonical_contigs(fa_regions)
access_regions = GA.from_rows(fa_regions)
for ex_fname in exclude_fnames:
excluded = tabio.read(ex_fname, 'bed3')
access_regions = access_regions.subtract(excluded)
return GA.from_rows(join_regions(access_regions, min_gap_size))