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#!/usr/bin/python3
"""
usage: %prog species1,species2,... nrequired < maf
"""
import sys
import bx.align.maf
from bx.cookbook import doc_optparse
SPAN = 100
MIN = 100
def main():
options, args = doc_optparse.parse(__doc__)
try:
species = args[0].split(",")
nrequired = int(args[1])
except Exception:
doc_optparse.exit()
maf_reader = bx.align.maf.Reader(sys.stdin)
interval_start = None
interval_end = None
for m in maf_reader:
ref = m.components[0]
# Does this alignment have enough of the required species
if nrequired <= len([comp for comp in m.components if comp.src.split(".")[0] in species]):
if interval_start is None:
interval_start = ref.start
interval_end = ref.end
else:
if ref.start - interval_end < SPAN:
interval_end = ref.end
else:
if interval_end - interval_start >= MIN:
print(ref.src.split(".")[1], interval_start, interval_end)
interval_start = ref.start
interval_end = ref.end
else:
if interval_start is not None and interval_end - interval_start >= MIN:
print(ref.src.split(".")[1], interval_start, interval_end)
interval_start = None
interval_end = None
if __name__ == "__main__":
main()
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