Python for Bioinformatics Fall 2014

Transcription

1 Python for Bioinformatics Fall 2014 Ntino Krampis, PhD Associate Professor Biological Sciences Class

2 Course Structure Meets weekly on Tuesdays 2-4pm Office hours on Mondays 10am - 12pm, will not answer anymore. Weekly homework due on day of class Will follow textbook as close as possible Homework is writing computer code for data data analysis: work in computer lab or your PC 2

3 Syllabus (Detailed syllabus on the Blackboard) : Introduction to Programming and first steps with Data Types in Python : Programming: More Data Types & Flow Control, : Basic Programming: Advanced Data Types & Flow Control : Bioinformatics: Parsing Files & Regular Expressions 3

4 Bioinformatics Joint field of Biology and Computer Science Use computer code for analysis of -omics datasets Interested in doing research in Bioinformatics: get a good grade in the class and join my lab 4

5 Computer Algorithms & Code Difference between an algorithm and code This is an algorithm 5

6 Computer Algorithms & Code This is computer code Computer code is instructions in computer language, on how to execute the steps of the algorithm. 6

7 Computer Algorithms & Code This is a bioinformatic algorithm and code 7

8 Computer Code in Python Python is a scripting language, code is called scripts Scripts are interpreted, line by line by the Python interpreter The interpreter can be interactive (good for learning or testing code) Or can run programs in batch, reading the code from a file (we will do this for homework) 8

9 The Python Interpreter Open the terminal in your Mac computer Either by clicking the icon on the dock Or by hitting cmd+space and search for terminal: 9

10 Python Variables: Strings Ntinos-MacBook-Pro:~ krampis$ python Python (default, Mar , 22:15:05) [GCC Compatible Apple LLVM 5.0 (clang )] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> print("hello World") Hello World >>> message = "Hello World" >>> print(message) Hello World >>> message = input() "Hello World >>> print(message) Hello World >>> greeting = "your message to the world?" >>> message = input(greeting) your message to the world? "Hello World" >>> print message Hello World 10

11 Python Variables: Integers >>> integer = 2 >>> print(integer) 2 >>> google = 2 >>> print(google) 2 >>> yahoo = "2" >>> print(yahoo) 2 >>> google / 2 1 >>> yahoo / 2 Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: unsupported operand type(s) for /: 'str' and int' >>> google**2 4 >>> string**2???? 11

12 String Quotations & Functions >>> dna = "ACGT" >>> print dna ACGT >>> dna = 'ACGT' >>> print dna ACGT >>> dna = "'ACGT'" >>> print dna ACGT >>> dna = " 'ACGT' ACGT >>> dna = ''' 'ACGT' 'ACGT' ''' >>> dna = 'ACGT' >>> dna.lower() acgt' >>> dna = 'ACgt' >>> dna.upper() ACGT >>> 2.upper()??? String quotes need to match on both sides Functions as built in to Python, and operate on specific data types 12

13 String Quotations & Functions >>> "ACGT".replace( 'A', 'T') TCGT' >>> "'ACGT'".replace( 'A', 'T') TCGT'" >>> import math >>> math.sqrt(2) >>> math.sqrt( 2 )??? >>> "Hello my name is Ntino".split() ['Hello', 'my', 'name', 'is', Ntino ] >>> name = Hello my name is Ntino >>> name.split() ['Hello', 'my', 'name', 'is', 'Ntino'] >>> "Hello, my name is, Ntino".split(',') ['Hello', ' my name is', ' Ntino ] >>> "Hello my name is Ntino".split(',') ['Hello my name is Ntino'] 13

14 String Quotations & Functions Python language reference, section

15 List Variables: >>> "Hello my name is Ntino".split() ['Hello', 'my', 'name', 'is', Ntino ] >>> list = [1, two",3,4,"last"] >>> nested_list = ["a string", list, 0] >>> print nested_list ['a string', [1, 'two', 3, 4, 'last'], 0] >>> nested_nest_list = ["a string", nested_list, 0, list] >>> print(nested_nest_list) ['a string', ['a string', [1, 'two', 3, 4, 'last'], 0], 0, [1, 'two', 3, 4, last']] >>> nested_nest_list = [] >>> print(nested_nest_list) [] 15

16 Operations with List Variables: >>> nucleic = ['A', 'C', 'G', T'] >>> nucleic[1] 'C' >>> nucleic[0] A' >>> nucleic[4] = 'U' Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: list assignment index out of range >>> nucleic.append('u') >>> print(nucleic) ['A', 'C', 'G', 'T', U'] >>> nucleic.pop() 'U' >>> print(nucleic) ['A', 'C', 'G', T'] >>> nucleic.append([1,2,3]) >>> print(nucleic) ['A', 'C', 'G', 'T', [1, 2, 3]] 16

17 Operations with List Variables: >>> print(nucleic) ['A', 'C', 'G', 'T', [1, 2, 3]] >>> nucleic[0:2] ['A', C'] >>> nucleic[0:3] ['A', 'C', G'] >>> nucleic[-1] [1, 2, 3] >>> nucleic.index('t') 3 >>> nucleic.index([1, 2, 3]) 4 17

18 Read Chapters 1(quick), Chapt. 2 up to 3.5 (critical) Do homework, due by next class 18