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#!/usr/bin/python
import sys
from pbsuite.utils.FileHandlers import M4File, M5File
if __name__ == '__main__':
try:
fn = sys.argv[1]
except:
sys.stderr.write(("Error! Expected One Argument, " \
"an m4 or m5 alignment file\n"))
exit(1)
if fn.endswith('.m4'):
file = M4File(sys.argv[1])
elif fn.endswith('.m5'):
file = M5File(sys.argv[1])
else:
print "Unrecognized File Type (expecting .m4 or .m5)"
exit(1)
if len(sys.argv) == 3:
out = open(sys.argv[2],'w')
else:
out = sys.stdout
out.write("\n".join(map(lambda x: x.toBed(), file))+"\n")
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