#! /usr/bin/python
  2 import re
  3 import sys
  4 import traceback
  5 from codon import Codon
  6
  7 #counters for the current line and index
  8 line = -1
  9 #lists for storing index positions
 10 pos_start = []
 11 pos_stop = []
 12 neg_start = []
 13 neg_stop = []
 14
 15 codon_list = [
 16   Codon('ATG'),
 17   Codon('GTG'),
 18   Codon('TAG'),
 19   Codon('TAA'),
 20   Codon('TGA'),
 21 ]
 22 # Codon('TAC'),
 23 # Codon('CAC'),
 24 # Codon('ATC'),
 25 # Codon('ATT'),
 26 # Codon('ACT')
 27 #]
 28
 29 def addToList(this_codon):
 30   """Sort out the codons and add the matching index to the respective list"""
 31   if this_codon == 'ATG' or this_codon == 'GTG':
 32     pos_start.append(index)
 33     #print "Codon: %s, %s, %d" % (co.codon_str, co.currFrame.tostring(),index)
 34   elif this_codon == 'TAG' or this_codon == 'TAA' or \
 35     this_codon == 'TGA':
 36       pos_stop.append(index)
 37       #print "Codon: %s, %s, %d" % (co.codon_str, co.currFrame.tostring(),index)
 38   elif this_codon == 'TAC' or this_codon == 'CAC':
 39     neg_start.append(index)
 40   else:
 41     neg_stop.append(index)
 44 dna_file = open('./NC_007577.fna')
 45 try:
 46   try:
 47     dna_file.readline()
 48     first_codon = dna_file.read(3)
 49     for co in codon_list:
 50       #print "This codon is: %s" % co.codon_str
 51       co.setFrame(first_codon)
 52       if co.match_found():
 53         addToList(co.codon_str)
 54     next_nuc = dna_file.read(1)
 55     index = 3
 56     while (next_nuc != '') and index < 5000: #while not end of file
 57       if (next_nuc != '\n'): #skip line ends, don't count them
 58         index += 1
 59         for co in codon_list:
 60           co.read_nucleotide(next_nuc)
 61           if co.match_found():
 62             addToList(co.codon_str)
 63             #print "%s found at %d" % (co, index)
 64       next_nuc = dna_file.read(1)
 65   except Exception, e:
 66     traceback.print_exc(file=sys.stderr)
 67     print "Unexpected error: %s" % e[0]
 68 finally:
 69   dna_file.close()
 70
 71 print "*********Preprocessing Complete**********"
 72