Data Structures

DNA Manipulation

In molecular biology, a DNA sequence can be represented by a string made up of the characters A, T, G and C. The length of a DNA sequence must also be a multiple of three.

Write a function is_dna(string) which returns True if the input is a valid DNA sequence and False otherwise.
```
 >>> is_dna("AATGAC")
 True
 >>> is_dna("ACtACT")
 False
 >>> is_dna("AATC")
 False
```
The reverse complement of a DNA sequence is computed by interchanging A with T, and G with C, and reversing the string. For example, the reverse complement of AATGAC is GTCATT. Write a function reverse_complement(dna) which returns the reverse complement of the sequence dna. If the sequence is invalid, return None.
```
 >>> reverse_complement("AATGAC")
 'GTCATT'
 >>> reverse_complement("GATTACAAA")
 'TTTGTAATC'
 >>> print(reverse_complement("GAGA"))
 None
```
A DNA sequence is divided up into blocks of three letters, called codons. For example, the sequence GATTACAAA contains three codons: GAT, TAC and AAA. Write a function print_codons(dna) which one-by-one prints each of the codons of the sequence dna. If the sequence is invalid, do nothing.
```
 >>> print_codons("GATTACAAA")
 GAT
 TAC
 AAA
 >>> print_codons("AATGAC")
 AAT
 GAC
 >>> print_codons("GAGA")
 >>>
```

Challenge: Returning Codons

In general, a function that performs a logical task, such as dividing a DNA sequence into codons, should not perform output from within the function. It is better to return the result and let the calling code determine what to do with the result. This makes it easier to reuse the function in other parts of a program. It also means that the code for outputting data is not spread throughout the logic of the program.

Write a generate_codons(dna) function that returns a list containing each of the codons of the sequence dna. If the sequence is invalid, return None. Modify the print_codons(codons) function so that the parameter is now a list containing the codons. Print each codon found in the list on a separate line, like in the previous implementation of print_codons(dna). For the purposes of this exercise, you may assume that the list contains a valid set of codons.

>>> generate_codons("GATTACAAA")
['GAT', 'TAC', 'AAA']
>>> result = generate_codons("GA")
>>> type(result)

<class 'NoneType'>

>>> print_codons(generate_codons("GATTACAAA"))
GAT
TAC
AAA
>>>

Aside: Dealing with Bad Input

If we encounter a string which is not an invalid DNA sequence, the optimal situation would be not to ‘ignore’ the invalid data by doing nothing, instead we should cause an error to occur, by raising an exception:

...
if ... :
    raise ValueError("Invalid DNA sequence")
...

We will cover raising and handling exceptions later in the course.

Number Extraction

Data mining is the process of discovering and analysing information from raw datasets. Often, most of the data is not relevant, and so the first task in data mining is to extract only the useful information. In this task, we are given a string that contains numbers, and we want to extract the first integer out of the string.

Write a function get_number(string) which returns the first positive integer in the string, or None if there are no integers in the string. You may find it useful to use the str.isdigit method.

>>> get_number("zbagy22.17clguba19")
22
>>> get_number("ubyl 014tenvy,1975 ncevy9gu")
14
>>> print(get_number("sylvatpvephf"))
None

Challenge: Negative Numbers

Modify this function to handle negative integers.

>>> get_number("zl-39u0irepensg")
-39
>>> get_number("vf-shyy23-4bs")
23
>>> get_number("33yf-")
33