Primitives

1

Simple Values

• logical (Boolean)• integer• float• string

– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'– "AARHQGRGAPCGESFWHWALGADGGHGHAQP"– """MKQLNFYKKN SLNNVQEVFS YFMETMIST"""– '''MWNSNLPKPN AIYVYGVANA NITFFKGSDI'''

• None

2

Expressions

• Numeric Operators• Logical Operations

– '' and "A''– 0 and 1 or 2– 'yes' if 2 - 1 else 'no'

• String Operations– 'TATA' in 'TATATATATATATATATATATATA'– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[0]– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[1:4]– MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[:8]– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[9:]

3

Expressions

4

0 1 2 3 4

T A A C G

-5 -4 -3 -2 -1

• String Operations– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[9:-1]– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[:]– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[16:0:-4]– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[16::-4]– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[::-1]

Calls

• Function calls– len('TATA')– print('AAT', 'AAC', 'AAG', 'AAA')

• Method calls– 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'.count('D

L')

5

Running Python interactively• Ctrl-A

– Go to the beginning of the line.• Ctrl-E

– Go to the end of the line.• Ctrl-B or left arrow

– Move one character to the left.• Ctrl-F or right arrow

– Move one character to the right.• Backspace

– Delete the preceding character.• Ctrl-D

– Delete the next character.• Ctrl-K

– Delete the rest of the line after the cursor.• Ctrl-Y

– “Yank” the last killed text into the line at the location of the cursor.• Ctrl-_ (underscore)

– Undo; can be repeated.• Ctrl-R

– Search incrementally for a preceding input line.• Ctrl-S

– Search incrementally for a subsequent input line.

6

Tracebacks

• NameError: 'Non' is not defined– Python doesn’t recognize a name (more on this in the

next chapter).

• IndexError: string index out of range– For a string of length N, an index (i.e., the value

between square brackets) must be in the range -N <= index < N-1.

• SyntaxError– Python syntax violation.

• ZeroDivisionError– /, //, or % with 0 as the second operand.

7

Names, Functions, and Modules

8

Names bound to objects

9

Names in different namespaces bound to objects

10

Assigning Names

11

Defining Functions

12

Function calls

13

Function returns

14

Do-nothing statement

15

Example

16

def validate_base_sequence(base_sequence):

"""Return True if the string base_sequence contains only upper- or lowercase T, C, A, and G characters, otherwise False"""

seq = base_sequence.upper()

return len(seq) == \

seq.count('A') + seq.count('G') + \

seq.count('T') + seq.count('C')

GC content of a given DNA sequencedef gc_content(base_seq):

17

GC content of a given DNA sequencedef gc_content(base_seq):

""""Return the percentage of G and C characters in base_seq"""

seq = base_seq.upper()

return (seq.count('G') + seq.count('C')) / len(seq)

18

Assertion

19

GC content of a given DNA sequencedef gc_content(base_seq):

"""Return the percentage of G and C characters in base_seq"""

assert validate_base_sequence(base_seq), \

'argument has invalid characters'

seq = base_seq.upper()

return ((base_seq.count('G') + base_seq.count('C')) /

len(base_seq))

20

Default Parameter Values

21

def validate_base_sequence(base_sequence, RNAflag=False):

"""Return True if the string base_sequence contains only upper- or lowercase T, C, A, and G characters, otherwise False"""

seq = base_sequence.upper()

return len(seq) == ( seq.count('A') +

seq.count('G') +

seq.count('U' if RNAflag else 'T') +

seq.count('C'))

Using Modules

22

Using Modules

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Using Modules

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from random import randint

def random_base(RNAflag = False):

return ('UCAG' if RNAflag else 'TCAG')[randint(0,3)]

def random_codon(RNAflag = False):

return random_base(RNAflag) + random_base(RNAflag) + random_base(RNAflag)

Python Files

25

def validate_base_sequence(base_sequence, RNAflag = False):"""Return True if the string base_sequence contains only upper- or lowercase T (or U, if RNAflag), C, A, and G characters, otherwise False"""seq = base_sequence.upper()return len(seq) == (seq.count('U' if RNAflag else 'T') +

seq.count('C') +seq.count('A') +seq.count('G'))

def gc_content(base_seq):"""Return the percentage of bases in base_seq that are C or G"""assert validate_base_sequence(base_seq), \

'argument has invalid characters'seq = base_seq.upper()return (base_seq.count('G') +base_seq.count('C')) / len(base_seq)

def recognition_site(base_seq, recognition_seq):"""Return the first position in base_seq where recognition_seqoccurs, or −1 if not found"""return base_seq.find(recognition_seq)

def test():

assert validate_base_sequence('ACTG')

assert validate_base_sequence('')

assert not validate_base_sequence('ACUG')

assert validate_base_sequence('ACUG', False)

assert not validate_base_sequence('ACUG', True)

assert validate_base_sequence('ACTG', True)

assert .5 == gc_content('ACTG')

assert 1.0 == gc_content('CCGG')

assert .25 == gc_content('ACTT')

print('All tests passed.')

test()

Python Files

• http://shared.tistory.com/79

26

Collections

27

compound

• they group together multiple objects• called collections or containers• Some collection types can even contain items

with a mixture of types, including other collections.

• sets - don’t allow individual access• sequences - use numerical indexes• mappings - use keys

28

Sets

• an unordered collection of items that contains no duplicates

• set('TCAGTTAT') -> set(['A', 'C', 'G', 'T'])

29

Sets

30

Sequences

• ordered collections that may contain duplicate elements

31

Sequences - String

• Testing– str1.isalpha()– str1.isalnum()– str1.isdigit()– str1.numeric()– str1.isdecimal()– str1.islower()– str1.isupper()– str1.istitle()

32

Sequences - String

• Searching– str1.startswith(str2[, startpos, [endpos]])– str1.endswith(str2[, startpos, [endos]])– str1.find(str2[, startpos[, endpos]])– str1.rfind(str2[, startpos[, endpos]])– str1.index(str2[, startpos[, endpos]])– str1.rindex(str2[, startpos[, endpos]])– str1.count(str2[, startpos[, endpos]])

33

Sequences - String

• Replacing– str1.replace(oldstr, newstr[, count])– str1.translate(dictionary)

• Changing case– str1.lower()– str1.upper()– str1.capitalize()– str1.title()– str1.swapcase()

34

Sequences - String

• Reformatting– str1.lstrip([chars])– str1.rstrip([chars])– str1.strip([chars])– str1.ljust(width[, fillchar])– str1.rjust(width[, fillchar])– fillchar (the default fill character is a space).– str1.center(width[, fillchar])– str1.expandtabs([tabsize])

35

Sequences - Tuples

• immutable sequence that can contain any type of element

• ('TCAG', 'UCAG')• bases = 'TCAG', 'UCAG'

36

Sequences - Lists

• mutable sequence of any kind of element

37

Sequences - Lists

38

Mappings

39

• mutable unordered collection of key/value pairs– associative arrays, lookup tables, and hash tables

The RNA amino acid translation table

40

Mappings - Dictionary

41

Mappings - Dictionary

42