Instructions for recursiveGenetics

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This task will give you practice with fruitful recursion. For most of the functions, it asks you to do the same thing you did in the earlier genetics task, but this time using recursion rather than loops.

Recall that in the genetics task, we were dealing with sequences of letters representing DNA and RNA bases, using the letters 'A', 'U', 'G', and 'C', along with 'T' instead of 'U' for DNA. You will be using these strings again in this assignment, and again, you don't need to know any of the details of the biology to get things to work.

There are four different functions you must write, which are equivalent to functions from the earlier genetics task. All functions in this assignment require you to use recursion, and conversely, you are not allowed to use any loops in these functions. The descriptions from the previous task have been repeated below, even though (except that you must use recursion) their required behavior is exactly identical to the previous task.

1. countOtherBases - This function takes two arguments — (1) a sequence of bases and (2) a particular base to exclude — and returns the number of bases (i.e., letters) in the sequence that are different from excluded base. These examples for countOtherBases show how it works.
2. templateSequence - Given a sequence of RNA bases, returns the sequence of DNA bases that must have been used to create that RNA sequence (i.e., the template for that piece of RNA). You must use the provided templateBase function to compute the DNA template base that corresponds to a single RNA base within this function. These examples for templateSequence demonstrate how it works.
3. onlyAU - Given an RNA sequence, returns a new sequence consisting of only the 'A' and 'U' bases from the original sequence with the 'C' and 'G' bases removed. These examples for onlyAU demonstrate how it must work.
4. transcriptionErrors - Given two sequences, one of RNA and one of DNA, looks for transcription errors where the base in the RNA sequence doesn't match the base in the DNA sequence. Each RNA base is supposed to be transcribed from a particular DNA base (for example, the DNA base 'A' becomes the RNA base 'U'), but sometimes errors occur in this process. Given an RNA sequence and the DNA it came from, any place where the corresponding bases aren't paired (according to the templateBase function) is a transcription error. This function must return the number of transcription errors evident in the given RNA and DNA pair. This example of transcriptionErrors demonstrates how this should work. For this function, you may NOT assume that the two strings provided will always be the same length, and if one is longer, in addition to counting errors in the portion where they overlap, each extra base in the longer string should count as an error, although we will only test this as an extra goal.

Once you have written these functions and have tested them to make sure they work correctly, you are done with this task. Refer to the examples below in understanding how these functions should work, and feel free to refer back to our solutions for the earlier genetics task which are available via the Potluck server.

Notes

• The genetics.py file contains a correct definition of the templateBase function that you must use in your definitions of templateSequence and transcriptionErrors
• For all the functions, you may assume that all of the arguments are valid, and do not need to handle any error cases. This means that:
  • You may assume that all DNA/RNA sequence arguments are strings with zero or more correct bases.
  • You may assume that any base argument is a single-character string that is a valid base.
• There are various requirements on the structure of each function which are expressed in the rubric, but are not described explicitly above. You should check the rubric before defining each function to see which other functions you may be required to use. In many cases there are also extra goals which require writing functions in a particular way, often by using only a recursive call, for example.
• As usual, you must document every function you write with a triple-quoted docstring after the function header.
• Also as usual, you must not waste fruit and you must not waste boxes.
• We have provided a testing file test_recursiveGenetics.py that you can use to test your code. You are encouraged to define extra tests beyond the few we've provided, since they are not sufficient to catch many kinds of errors you might encounter.