#!/usr/bin/python
"""Platform-independent script for removing or replacing quoted strings.

python removeQuoted.py <infile> <outfile> [-D<name>=<value>]

first argument in input file path (default is std in)
second argument is ouput file path (default is std out).
any arguments of the form -D<name>=<value> are treated as variable definitions 
Currently:
    - uses @ as the quote character
    - if text between quote characters matches a variable defined on the command line
    it will be replaced with the value, otherwise its replaced with nothing.
    - demands that the quoted string is on a single line
    - does not have any mechanism for escaping the @
    - does not replace consecutive @'s or strings that are started with multiple
        @ symbols (this is a concession to the @@@ replacement syntax of the 
        CIPRES registry).
"""
import re
import sys
definitions = {}
for arg in sys.argv[1:] :
    if arg.startswith("-D") and len(arg) > 2 :
        nv = arg[2:].split("=", 1)
        if len(nv) == 2:
            definitions[nv[0]] = nv[1]
        sys.argv.remove(arg)    

         
#set inStream 
if len(sys.argv) > 1:
    inFN = sys.argv[1]
    if inFN.upper() in ['-H', '--HELP', '-V', '--VERSION', '--VERBOSE']:
        sys.exit(__doc__)
    try:
        inStream = open(inFN, 'rU')
    except:
        sys.exit('Could not open %s' % inFN)
else:
    inStream = sys.stdin

#set outStream
if len(sys.argv) > 2:
    outFN = sys.argv[2]
    if outFN == inFN:
        sys.exit('Input and output files cannot be the same')
    try:
        outStream = open(outFN, 'w')
    except:
        sys.exit('Could not open %s' % infN)
else:
    outFN = None
    outStream = sys.stdout

try:
    #pattern = re.compile(r'@[^@]*@')
    pattern = re.compile(r'(?<=[^@])@([^@]+)@')  # this pattern is used to avoid replacing the @@@ strings that used to be replaced by the @    
      
    for line in inStream:
        value = ""
        m = pattern.search(line)
        if m and m.group(1) in definitions:
            value = definitions[m.group(1)]
        outStream.write(pattern.sub(value, line))
finally:
    if outFN is not None:
        outStream.close()