#! /usr/bin/env python
# from __future__ import division # / operator performs float rather than int division

import os, sys, string, cp, re

def main():
	"""
%(filename)s

Make filenames unix safe. Replaces all whitespace and non-alphanumeric 
charaters with a char specified in c.

{{k			check - print old name and new name with out making changes}}
{{c			replace with this character
	_}}
{{h			Prints documentation.}}
{{v			verbosity 
	1}}
{{version   print version info and exit}}

%(version)s
"""
	debug = 0

	# copy from here...
	docstringdict = {'filename':os.path.split(sys.argv[0])[-1],
	'version':'$Id: unixname.py,v 1.1 2004/10/10 02:53:10 nghoffma Exp $'}
	
	optlist, formattedDocString, formattedSummary = cp.optStringParser(main.__doc__ % docstringdict,
		optWidth=15, lineWidth=60, valOffset = 4, putVals=1)	
	dict = cp.commandparser(options=optlist, usage='Options:\n' + formattedSummary, 
		debug = debug, exitWithUsage=1)
		
	if dict.status('version'):
		sys.exit( 'Version: %(version)s\n' % docstringdict )
	#...to here

	if dict.status('h'):
		print formattedDocString
		sys.exit( 0 )
	v = dict.value('v')
	check = dict.status('k')
	replchar = dict.value('c')
		
	#read from a list of fasta files
	file_list = dict.value('infile_list', 'in')
	
	removeCrapRexp = re.compile(r'[\W\s]+')
	
	for file in file_list:
		name, ext = os.path.splitext(file)
		newname = removeCrapRexp.sub(replchar, name) + ext
		if v:
			print '%s --> %s' % (file, newname)
		if check:
			print 'skipping...'
			continue
		os.rename(file, newname)
		
		
		
if __name__ == '__main__':
	main()