ChunkManager1.py

import random
import ExtraModules

# Object that effectively manages RAM by addding bases to the file as soon as chunk is detected
# dnaBaseStr ---> our DNA encoded string
# currLenOfDNA ---> present length of DNA encoded
# chunkIndex ---> present chunkIndex
# fileID ---> represents ID of the file
# fileFinal ---> file Object for writing the final output 
# startIndex ---> actual DNA encoded string is from startIndex to end of dnaBaseStr
# maxRamCapacity ---> as soon as dnaBaseStr length is more than maxRamCapacity it empties strings and adjust startIndex accordingly
class ChunkManager(object):
  dnaBaseStr = []
  currLenOfDNA = 0
  chunkIndex = 0
  fileID = ''
  fileFinal = None 
  startIndex = 0
  maxRAMCapacity = 500000

  def addBase(self,base1):
    self.dnaBaseStr.append(base1)
    self.currLenOfDNA = self.currLenOfDNA + 1
    if self.currLenOfDNA == 100 :
       self.updateManager()
  def addString(self,string1):
     for base in string1:
        self.addBase(base)

  def updateManager(self):
     currChunk = ''.join(self.dnaBaseStr[self.startIndex:])
     if (self.chunkIndex)%2 != 0 :
       currChunk = ExtraModules.reverseComplement(currChunk)

     i3 = ExtraModules.intToBase3(self.chunkIndex,12) 
     P = int(self.fileID[0]) + int(i3[0]) + int(i3[2]) + int(i3[4]) + int(i3[6]) + int(i3[8]) + int(i3[10])
     P = P % 3
     indexingInfo =  self.fileID + i3 + str(P)
     encodedIndexInfo = ExtraModules.encodeSTR(indexingInfo,currChunk[-1])

     if currChunk[0] == 'A' :
        startBase = 'T'
     elif currChunk[0] == 'T' :
        startBase = 'A'
     else :
        randomNum = random.random()
        if randomNum > 0.5:
          startBase = 'A'
        else:
          startBase = 'T'

     if encodedIndexInfo[-1] == 'C' :
        endBase = 'G'
     elif encodedIndexInfo[-1] == 'G' :
        endBase = 'C'
     else :
        randomNum = random.random()
        if randomNum > 0.5 :
          endBase = 'C'
        else:
          endBase = 'G'

     currChunk = startBase + currChunk + encodedIndexInfo + endBase 

     self.chunkIndex = self.chunkIndex + 1
     self.startIndex = self.startIndex + 25
     self.currLenOfDNA = 75
     if self.startIndex >= self.maxRAMCapacity :
        self.dnaBaseStr = self.dnaBaseStr[self.startIndex:]
        self.startIndex = 0
     self.fileFinal.write(unicode(currChunk+'\n'))
     
  def close(self):
     if self.currLenOfDNA > 0:
        self.updateManager()
     if self.fileFinal is not None:
        self.fileFinal.flush()
        self.fileFinal.close()

  def __init__(self,fileFinal1,fileID1):
     self.fileFinal = fileFinal1
     self.fileID = fileID1
     self.dnaBaseStr = []
     self.currLenOfDNA = 0
     self.chunkIndex = 0
     self.startIndex = 0
     self.maxRAMCapacity = 500000