Containers: Tuples and Comprehensions

Authors:	Tom Dunham
Date:	2009-03-31

Container Types

Tuples are immutable lists.

>>> tu = (2, 3, 5, 7)
>>> tu
(2, 3, 5, 7)

>>> tu.append(11)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'tuple' object has no attribute 'append'

Unpacking

>>> def botright(x, y, w, h):
...     return x+w, y+h
...
>>> botright(10, 10, 2, 2)
(12, 12)

>>> x, y = botright(10, 10, 2, 2)
>>> x
12
>>> y
12

Tuple unpacking is useful in for loops

for condon, aa in [('CTT', 'L'), ('TAG', '_'), ('ACA', 'T'), ('ACG', 'T'), ('ATC', 'I')]:
   ...

>>> foo = []
>>> bar = (1, foo, "three")
>>> bar
(1, [], 'three')

>>> foo.append(222)

>>> bar
(1, [222], 'three')

Remember containers use identity

We've written a lot of loops like this:

acc = []
for i in sequence:
    newi = do_something_with(i)
    acc.append(newi)

A list comprehension is more concise

acc = [do_something_with(i) for i in sequence]

>>> li = [3, 5, 7, 11]
>>> li
[3, 5, 7, 11]

>>> li2 = [2 * i for i in li]

>>> li2
[6, 10, 14, 22]
>>> li
[3, 5, 7, 11]

Slices

>>> [2 * i for i in li[1:3]]
[10, 14]

Strings

>>> [i.upper() for i in ("foo", "bar", "baz")]
['FOO', 'BAR', 'BAZ']

We've also written a lot of loops following this pattern

acc = []
for i in sequence:
    if test(i):
        newi = do_something_with(i)
        acc.append(newi)

This can be written

acc = [do_something_with(i) for i in sequence if test(i)]

>>> li
[3, 5, 7, 11]
>>> [2 * i for i in li if i > len(li)]
[10, 14, 22]

See handout

Rewrite your solution to Q3 from lecture 4 (mapping condon to amino acid) using list comprehensions
Write a function ispalindromic that tests if a sequence is palindromic (returning True if it is a palindrome and False if not).
Write a function that takes a DNA sequence and returns a list of tuples containing enzyme name and the location of the restriction site for every palindromic restriction site. Use the following list of enzymes:
```
EcoRI  GAATTC
EcoRII  CCWGG
BamHI  GGATCC
HindIII  AAGCTT
TaqI  TCGA
NotI  GCGGCCGC
HinfI  GANTC
Sau3A  GATC
PovII  CAGCTG
SmaI  CCCGGG
HaeIII  GGCC
AluI  AGCT
EcoRV  GATATC
KpnI  GGTACC
PstI  CTGCAG
SacI  GAGCTC
SalI  GTCGAC
ScaI  AGTACT
SphI  GCATGC
StuI  AGGCCT
XbaI  TCTAGA
```
- You can use triple-quotes (""") for multi-line strings, and the strip and splitlines string methods to turn this list into a data structure you can use.
- You may find the pprint function from the pprint module useful to inspect the data structures you build.
- Use this function to load a test sequence (we'll study reading from files in the next section)
```
def loadseq(fn="coursefiles\\sample.dna"):
    return open(fn).read().replace(" ", "").upper()
```
Turn this list of tuples into an index - a dictionary where the keys are enzyme names and the values are lists of locations