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#!/usr/bin/python3
"""
Complement the regions of a bed file. Requires a file that maps source names
to sizes. This should be in the simple LEN file format (each line contains
a source name followed by a size, separated by whitespace).
usage: %prog bed_file chrom_length_file
"""
from bx.bitset_builders import binned_bitsets_from_file
from bx.cookbook import doc_optparse
def read_len(f):
"""Read a 'LEN' file and return a mapping from chromosome to length"""
mapping = {}
for line in f:
fields = line.split()
mapping[fields[0]] = int(fields[1])
return mapping
options, args = doc_optparse.parse(__doc__)
try:
in_fname, len_fname = args
except Exception:
doc_optparse.exit()
bitsets = binned_bitsets_from_file(open(in_fname))
lens = read_len(open(len_fname))
for chrom in lens:
if chrom in bitsets:
bits = bitsets[chrom]
bits.invert()
len = lens[chrom]
end = 0
while True:
start = bits.next_set(end)
if start == bits.size:
break
end = bits.next_clear(start)
if end > len:
end = len
print("%s\t%d\t%d" % (chrom, start, end))
if end == len:
break
else:
print("%s\t%d\t%d" % (chrom, 0, lens[chrom]))
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