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#!/usr/bin/python3
"""
Mask out potential CpG sites from a maf. Restricted or inclusive definition
of CpG sites can be used. The total fraction masked is printed to stderr.
usage: %prog < input > output
-m, --mask=N: Character to use as mask ('?' is default)
-r, --restricted: Use restricted definition of CpGs
"""
import sys
import bx.align
import bx.align.maf
import bx.align.sitemask.cpg
from bx.cookbook import doc_optparse
def main():
options, args = doc_optparse.parse(__doc__)
try:
if options.mask:
mask = options.mask
else:
mask = "?"
except Exception:
doc_optparse.exception()
reader = bx.align.maf.Reader(sys.stdin)
writer = bx.align.maf.Writer(sys.stdout)
if options.restricted:
cpgfilter = bx.align.sitemask.cpg.Restricted(mask=mask)
else:
cpgfilter = bx.align.sitemask.cpg.Inclusive(mask=mask)
cpgfilter.run(reader, writer.write)
print(str(float(cpgfilter.masked) / float(cpgfilter.total) * 100) + "% bases masked.", file=sys.stderr)
if __name__ == "__main__":
main()
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