#!/usr/bin/env python

"""
 May 31, 2013, Dr. Brian Fristensky, University of Manitoba

 Description: This is a front end for mrtrans. It makes sure that the names of
 the sequences in PROTFILE and DNAFILE are the same, and re-orders
 the sequences in DNAFILE, if necessary, to be in the same order
 as in PROTFILE.
 This script assumes that sequence names in PROTFILE are IDENTICAL to
 the corresponding names in DNAFILE.

 Synopsis: mrtrans.py protfile dnafile

 Files: protfile   fasta file with multiply aligned proteins

        dnafile    fasta file with unaligned DNA sequences

@modified: May 31, 2013
@author: Brian Fristensky
@contact: frist@cc.umanitoba.ca
"""

import sys
import os

blib = os.environ.get("BIRCHPYLIB")
sys.path.append(blib)

from birchlib import Birchmod
from birchlib import Argument

PROGRAM = "mrtrans.py : "
USAGE = "\n\tUSAGE: mrtrans.py protfile dnafile"
BM = Birchmod(PROGRAM, USAGE)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class Parameters:
    "Wrapper class for command line parameters"
    def __init__(self):
        """
     	  Initializes arguments:
     		PFN=""
     		DFN=""
     	  Then calls read_args() to fill in their values from command line
          """
        self.PFN = ""
        self.DFN = ""
        self.read_args()
	
    def read_args(self):
        """
		Read command line arguments into a Parameter object
		"""
	
        length = len(sys.argv)
	
        protfile = Argument("", str, BM)
        dnafile = Argument("", str, BM)
	
        protfile.set_position(length-2)
        dnafile.set_position(length-1)
			
	
        try:
            self.PFN = protfile.fetch()
            self.DFN = dnafile.fetch()
		
		
        except ValueError:
            BM.printusage()
	
	
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class FILE:
    "Wrapper class for files"
     
    def __init__(self, FILENAME, MODE):
        """
          @param FILENAME: The name of the file
          @type FILENAME: str
          @param MODE: Type of file operation (read/write)
          @type MODE:str : (r, w, rw)
          """
        self.FN = FILENAME
	  
        self.LINE = "" # most recent line read
        try:
            self.F = open(FILENAME, MODE)
	  	
        except:
            BM.fileError(FILENAME)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class Sequence:
    def __init__(self):
        """
     	Holds name and sequence	
     		"""     
        self.Name = ""
        self.Seq=""

class SeqData:
    def __init__(self):
        """
     	Holds sequences and associated data	
     		""" 
	self.SeqLst = []  #list of sequences		    
	self.NumSeq = 0 # number of sequences
	self.SeqLen = 0 #length of sequences (all must be the same)
	self.NumEnz = 0 #number of rest. enzymes, primrily used by RESTML

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -



	      
	        
#======================== MAIN PROCEDURE ==========================


def main():
    """
 	Called when not in documentation mode.
 	"""
#---------- Set global variables	
P = Parameters ()

print "Protein file: " + P.PFN
print "DNA file: " + P.DFN

NAMEFLAG = '>'  # 1st character on the name line, indicating
    # the beginning of the next data list

# Read the protein alignment and unaligned DNA files

# Remove extraneous fields and characters from names so that they can be compared

# Make sure that, for every protein in protfile, there is a sequence with the 
# identical name in dnafile.

# Run mrtrans, sending output to a file

# Remove extraneous characters from the mrtrans output file
	
	
BM.exit_success()

if (BM.documentor() or "-test" in sys.argv):
    pass
else:
    main()