As we introduced a lot of new concepts it is important that you practice them.

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hands_on Exercise 7

Write a program that does the following:

1. Ask the user for a full DNA sequence
   • Make sure the sequence contains only GACT
2. Once you have a valid sequence
   • For each DNA fragment the user enters:
     • Check if it occurs in the full sequence
     • Print out the sequence position if so
     • Track each fragment
   • Keep on asking the user for DNA fragments, stop if they just press return
3. As a summary, print out all fragments with their position that you tracked

Tips to complete this exercise in case you get stuck.

• Use while loops: you can use the condition to decide when to end the loop depending on the user input
• Track the sequence fragment and position data using a list
• Use string methods!

• To check the full DNA sequence, you can count how many times each GACT letter occurs, add up these counts, and compare this value to the total length of the full DNA sequence

  solution Solution

  # This variable will be used for the while loop
  validSequence = False
   
  # Keep on going as long as the DNA sequence is not valid
  while not validSequence:
      # Get a string from the user
      fullDnaSequence = input("Please enter your full DNA sequence:")
      fullDnaSequence = fullDnaSequence.upper()
      
      # Count the GACT characters in the sequence
      gactCount = 0
      for code in 'GACT':
          gactCount += fullDnaSequence.count(code)
   
      # Check if the number of GACT characters matches the full length of the sequence
      # and set validSequence to True if so - this will stop the while: loop
      if gactCount == len(fullDnaSequence):
          validSequence = True
      else:
          print("\nInvalid sequence, only GACT allowed, try again!.\n")
  
  # Print some line breaks
  print("\n\n")
   
  # Prime the list to track the DNA fragments and the variable for the while loop
  dnaFragmentInfo = []
  dnaFragment = input("Please give a DNA fragment to check:")
   
  while dnaFragment:
      
      # Check if present at all
      dnaFragmentCount = fullDnaSequence.count(dnaFragment)
      if dnaFragmentCount:
          currentDnaSequenceIndex = 0
          for i in range(dnaFragmentCount):        
              # Equivalent to currentDnaSequenceIndex = currentDnaSequenceIndex + fullDna...
              currentDnaSequenceIndex += fullDnaSequence[currentDnaSequenceIndex:].index(dnaFragment)
   
              print("\n  Fragment {} present at position {}.\n".format(dnaFragment,currentDnaSequenceIndex + 1))
              dnaFragmentInfo.append((currentDnaSequenceIndex + 1,dnaFragment))
              currentDnaSequenceIndex += 1
      else:
          print("\n  Fragment {} not present!\n".format(dnaFragment))
   
      dnaFragment = input("Please give a DNA fragment to check:")
  
  # Print some line breaks
  print("\n\n")
  
  # Print out the fragment information again, first sort it
  dnaFragmentInfo.sort()
  for (dnaFragmentPosition,dnaFragment) in dnaFragmentInfo:
      print("Found {} at position {}".format(dnaFragment,dnaFragmentPosition))
  

Useful literature

Further information, including links to documentation and original publications, regarding the tools, analysis techniques and the interpretation of results described in this tutorial can be found here.