text: #!/usr/bin/python
  #-------------------------------------------------------------------------------
  # The MIT License (MIT)
  #
  # Copyright (c) 2015-16 Scripps Institute (USA) - Dr. Benjamin Good
  #                       STAR Informatics / Delphinai Corporation (Canada) - Dr. Richard Bruskiewich
  #
  # Permission is hereby granted, free of charge, to any person obtaining a copy
  # of this software and associated documentation files (the "Software"), to deal
  # in the Software without restriction, including without limitation the rights
  # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  # copies of the Software, and to permit persons to whom the Software is
  # furnished to do so, subject to the following conditions:
  #
  # The above copyright notice and this permission notice shall be included in
  # all copies or substantial portions of the Software.
  #
  # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  # THE SOFTWARE.
  #-------------------------------------------------------------------------------
  #
  # This Python script cleans up ill-formed KB 3.0 data input files 
  # which have the following problematic content:
  #
  # 1) Non-escaped single or double quotation marks
  # 2) Surplus embedded white space
  # 3) Empty lines (deleted)
  #
  import sys
  import codecs
  import re
  
  if len(sys.argv)<2:
  	print >>sys.stderr,"Usage: kb3_V5_preprocessor.py <inputfile>\n\nCreates a new version of the file with the\nsuffix '_clean' added to the input file name.\n"
  	exit(1)
  
  inputfilename=sys.argv[1]
  outputfilename = inputfilename+"_cleaned"
  
  with codecs.open(outputfilename, encoding='utf-8', mode='w' ) as output:
  
  	with codecs.open(inputfilename, encoding='utf-8', mode = 'r' ) as input:
  
  		for line in input:
  
  			line = line.strip()
  			if not len(line)>0: continue
  			
  			fields = line.split("\t")
  			record = None
  			for field in fields:
  				# strip off any flanking double quotes
  				field = field.strip('"') 
  	
  				# tweak internal (double) quotes
  				field = field.replace("'","''")
  				field = field.replace('"','""')
  				
  				# collapse whitespace except tabs to single space character
  				field = re.sub(r'[ \n\r\f\v]+'," ",field,flags=re.UNICODE)
  			
  				# add back in flanking double quotes
  				field = '"'+field+'"'
  				
  				if not record:
  					record = field
  				else:
  					record += "\t"+field
  			
  			print >>output, record
  