Numbers, lists and tuples

1
Numbers, lists and tuples

• Genome 559 Introduction to Statistical and
  Computational Genomics
• Prof. William Stafford Noble

2
Numbers

• Python defines various types of numbers
• Integers (1234)
• Floating point numbers (12.34)
• Octal and hexadecimal numbers (0177, 0x9gff)
• Complex numbers (3.04.1j)
• You will likely only need the first two.

3
Conversions

• gtgtgt 6/2
• 3
• gtgtgt 3/4
• 0
• gtgtgt 3.0/4.0
• 0.75
• gtgtgt 3/4.0
• 0.75
• gtgtgt 34
• 12
• gtgtgt 3.04.0
• 12.0

• The result of a mathematical operation on two
  numbers of the same type is a number of that
  type.
• The result of an operation on two numbers of
  different types is a number of the more complex
  type.
• integer ? float
• float ? complex

4
Formatting numbers

• The operator formats a number.
• The syntax is
• ltformat stringgt ltnumbergt
• gtgtgt f 3
• 3.000000
• gtgtgt .2f 3
• 3.00
• gtgtgt 5.2f 3
• 3.00

5
Conversion codes

• d integer
• f decimal value
• e scientific notation
• g easily readable notation (i.e., use decimal
  notation unless there are too many zeroes, then
  switch to scientific notation)

6
More complex conversions

• flagswidth.precisioncode

d, f, e, g
Number of digits after decimal
Total width of field
Left justify (-) Include numeric sign
() Fill in with zeroes (0)
7
Examples

• gtgtgt x 7718
• gtgtgt d x
• 7718
• gtgtgt -6d x
• 7718
• gtgtgt 06d x
• 007718
• gtgtgt x 1.23456789
• gtgtgt d x
• 1
• gtgtgt f x
• 1.234568
• gtgtgt e x
• 1.234568e00
• gtgtgt g x
• 1.23457
• gtgtgt g (x 10000000)
• 1.23457e07

8
Lists

• A list is an ordered string of objects
• gtgtgt myString Hillary
• gtgtgt myList Hillary, Barack, John
• Lists are
• ordered left to right
• indexed like strings (from 0)
• mutable
• heterogeneous
• gtgtgt list1 0, 1, 2
• gtgtgt list2 A, B, C
• gtgtgt list3 D, E, 3, 4
• gtgtgt list4 list1, list2, list3
• gtgtgt list4
• 0, 1, 2, A, B, C, D, E, 3, 4

9
Lists and strings are similar

• Lists
• gtgtgt L "adenine", "thymine" "cytosine",
  "guanine"
• gtgtgt L "adenine", "thymine", "cytosine",
  "guanine"
• gtgtgt print L0
• adenine
• gtgtgt print L-1
• guanine
• gtgtgt print L2
• 'cytosine', 'guanine'
• gtgtgt L 3
• 'adenine', 'thymine', 'cytosine', 'guanine',
  'adenine', 'thymine', 'cytosine', 'guanine',
  'adenine', 'thymine', 'cytosine', 'guanine'
• gtgtgt L9
• Traceback (most recent call last)
• File "ltstdingt", line 1, in ?
• IndexError list index out of range

• Strings
• gtgtgt s 'A''T''C''G'
• gtgtgt s "ATCG"
• gtgtgt print s0
• A
• gtgtgt print s-1
• G
• gtgtgt print s2
• CG
• gtgtgt s 3
• 'ATCGATCGATCG'
• gtgtgt s9
• Traceback (most recent call last) File
  "ltstdingt", line 1, in ? IndexError string index
  out of range

10
Lists can be changedstrings are immutable.

• Lists
• gtgtgt L "adenine", "thymine", "cytosine",
  "guanine"
• gtgtgt print L
• 'adenine', 'thymine', 'cytosine', 'guanine'
• gtgtgt L1 "uracil"
• gtgtgt print L
• 'adenine', 'uracil', 'cytosine', 'guanine'
• gtgtgt L.reverse()
• gtgtgt print L
• 'guanine', 'cytosine', 'uracil', 'adenine'
• gtgtgt del L0
• gtgtgt print L
• 'cytosine', 'uracil', 'adenine'

• Strings
• gtgtgt s "ATCG"
• gtgtgt print s
• ATCG
• gtgtgt s1 "U"
• Traceback (most recent call last)
• File "ltstdingt", line 1, in ?
• TypeError object doesn't support item assignment
• gtgtgt s.reverse()
• Traceback (most recent call last)
• File "ltstdingt", line 1, in ?
• AttributeError 'str' object has no attribute
  'reverse'

11
More list operations and methods

• gtgtgt L "thymine", "cytosine", "guanine"
• gtgtgt L.insert(0, "adenine")
• gtgtgt print L
• 'adenine', 'thymine', 'cytosine', 'guanine'
• gtgtgt L.insert(2, "uracil")
• gtgtgt print L
• 'adenine', 'thymine', 'uracil', 'cytosine',
  'guanine'
• gtgtgt print L2
• 'adenine', 'thymine'
• gtgtgt L2 "A", "T"
• gtgtgt print L
• 'A', 'T', 'uracil', 'cytosine', 'guanine'
• gtgtgt L2
• gtgtgt print L
• 'uracil', 'cytosine', 'guanine'
• gtgtgt L A, T, C, G
• gtgtgt L.index('C')
• 2
• gtgtgt L.remove('C')

12
Methods for expanding lists

• gtgtgt data make an empty list
• gtgtgt print data
• gtgtgt data.append("Hello!") append means "add to
  the end"
• gtgtgt print data
• 'Hello!'
• gtgtgt data.append(5)
• gtgtgt print data
• 'Hello!', 5
• gtgtgt data.append(9, 8, 7) append the list to
  end of list
• gtgtgt print data
• 'Hello!', 5, 9, 8, 7
• gtgtgt data.extend(4, 5, 6) extend means append
  each element
• gtgtgt print data
• 'Hello!', 5, 9, 8, 7, 4, 5, 6
• gtgtgt
• gtgtgt print data2
• 9, 8, 7
• gtgtgt print data20

13
Turn a string into a list

• ltstringgt.split(x) or use list(S)
• gtgtgt protein "ALA PRO ILE CYS"
• gtgtgt residues protein.split() split() uses
  whitespace
• gtgtgt print residues
• 'ALA', 'PRO', 'ILE', 'CYS'
• gtgtgt list(protein) list explodes each char
• 'A', 'L', 'A', ' ', 'P', 'R', 'O', ' ', 'I',
  'L', 'E', ' ', 'C', 'Y', 'S'
• gtgtgt print protein.split()
• 'ALA', 'PRO', 'ILE', 'CYS'
• gtgtgt protein2 "HIS-GLU-PHE-ASP"
• gtgtgt protein2.split("-") split using a
  delimiter
• 'HIS', 'GLU', 'PHE', 'ASP'

14
Turn a list into a string

• join is the opposite of split
• ltdelimitergt.join(L)
• gtgtgt L1 "Asp", "Gly", "Gln", "Pro", "Val"
• gtgtgt print "-".join(L1)
• Asp-Gly-Gln-Pro-Val
• gtgtgt print "".join(L1)
• AspGlyGlnProVal
• gtgtgt L2 "\n".join(L1)
• gtgtgt L2
• 'Asp\nGly\nGln\nPro\nVal'
• gtgtgt print L2
• Asp
• Gly
• Gln
• Pro
• Val

The order is confusing. - String to join with
is first. - List to be joined is second.
15
Tuples immutable lists

• Tuples are immutable.
• Why? Sometimes you want to guarantee that a list
  wont change.
• Tuples support operations but not methods.
• gtgtgt T (1,2,3,4)
• gtgtgt T4
• (1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4)
• gtgtgt T T
• (1, 2, 3, 4, 1, 2, 3, 4)
• gtgtgt T
• (1, 2, 3, 4)
• gtgtgt T1 4
• Traceback (most recent call last)
• File "ltstdingt", line 1, in ?
• TypeError object doesn't support item assignment
• gtgtgt x (T0, 5, "eight")
• gtgtgt print x
• (1, 5, 'eight')
• gtgtgt y list(x) converts a tuple to a list

16

• Basic list operations
• L 'dna','rna','protein' list assignment
• L2 1,2,'dogma',L list hold different
  objects
• L22 'central' change an element (mutable)
• L202 'ACGT' replace a slice
• del L01 'nucs' delete a slice
• L2 L concatenate
• L23 repeat list
• Lxy define the range of a list
• len(L) length of list
• ''.join(L) convert a list to string
• S.split(x) convert string to list- x
  delimited
• list(S) convert string to list - explode
• list(T) converts a tuple to list
• Methods
• L.append(x) add to the end
• L.extend(x) append each element from x to
  list
• L.count(x) count the occurences of x

17
Sample problem 1

• Write a program called dna-composition.py that
  takes a DNA sequence as the first command line
  argument and prints the number of As, Cs, Gs
  and Ts.
• gt python dna-composition.py ACGTGCGTTAC
• 2 As
• 3 Cs
• 3 Gs
• 3 Ts

18
Solution 1

• import sys
• sequence sys.argv1.upper()
• print sequence.count(A), As
• print sequence.count(C), Cs
• print sequence.count(G), Gs
• print sequence.count(T), Ts

19
Sample problem 2

• The melting temperature of a primer sequence can
  be estimated as
• T 2 ( of A or T nucleotides) 4 ( of G
  or C nucleotides)
• Write a program melting-temperature.py that
  computes the melting temperature of a given DNA
  sequence.
• gt python melting-temperature.py ACGGTCA
• 22

20
Solution 2

• import sys
• sequence sys.argv1.upper()
• numAs sequence.count('A')
• numCs sequence.count('C')
• numGs sequence.count('G')
• numTs sequence.count('T')
• temp (2 (numAs numTs)) (4 (numGs
  numCs))
• print temp

21
Sample problem 3 (optional)

• The object sys.argv is a list of strings.
• Write a program reverse-args.py that removes the
  program name from the beginning of this list and
  then prints the remaining command line arguments
  in reverse order with asterisks in between.
• gt python reverse-args.py 1 2 3
• 321

22
Solution 3

• import sys
• args sys.argv1
• args.reverse()
• print "".join(args)

23
Reading

• Chapters 9-12 of Learning Python (3rd edition) by
  Lutz.