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#!/usr/bin/python3
"""
Remove any blocks from a maf that overlap any of a set of intervals.
usage: %prog interval files... < maf
"""
import sys
import bx.align.maf
from bx import intervals
from bx.cookbook import doc_optparse
def __main__():
options, args = doc_optparse.parse(__doc__)
try:
assert len(args) > 0
except AssertionError:
doc_optparse.exit()
# Load Intervals
intersector = intervals.Intersecter()
for f in args:
for line in open(f):
if line.startswith("#") or line.isspace():
continue
fields = line.split()
intersector.add_interval(intervals.Interval(int(fields[0]), int(fields[1])))
# Start MAF on stdout
out = bx.align.maf.Writer(sys.stdout)
# Iterate over input MAF
for maf in bx.align.maf.Reader(sys.stdin):
# Find overlap with reference component
intersections = intersector.find(maf.components[0].start, maf.components[0].end)
# Write only if no overlap
if len(intersections) == 0:
out.write(maf)
# Close output MAF
out.close()
if __name__ == "__main__":
__main__()
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