text: #!/afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.7
  """
  Application to convert LAV file to AXT file. Reads a LAV file from standard 
  input and writes a AXT file to standard out;  some statistics are written 
  to standard error.
  
  usage: lav_to_axt [--silent] [path=replacement] < lav_file > axt_file
  """
  
  __author__ = "Bob Harris (rsharris@bx.psu.edu)"
  
  import sys
  import copy
  import bx.align.lav
  import bx.align.axt
  
  def usage(s=None):
  	message = __doc__
  	if (s == None): sys.exit (message)
  	else:           sys.exit ("%s\n%s" % (s,message))
  
  
  def main():
  
  	# parse the command line
  
  	silent = False
  	pathSubs = []
  
  	for arg in sys.argv[1:]:
  		if ("=" in arg):
  			ix = arg.find("=")
  			pathSubs.append((arg[:ix],arg[ix+1:]))
  		elif (arg == "--silent"):
  			silent = True
  		else:
  			usage("unrecognized argument: " + arg)
  
  	# read the alignments and other info
  
  	out = bx.align.axt.Writer(sys.stdout)
  
  	lavsRead = axtsWritten = 0
  	for lavBlock in bx.align.lav.Reader(sys.stdin,path_subs=pathSubs):
  		lavsRead += 1
  
  		out.write (lavBlock)
  		axtsWritten += 1
  
  	if (not silent):
  		sys.stderr.write ("%d blocks read, %d written\n" % (lavsRead,axtsWritten))
  
  
  if __name__ == "__main__": main()
  
  