Intro to Python

1
Intro to Python

• Foundations in Computational Biology II
• Spring 09
• TA Hannah Carter

2
Getting Started

• Type python at the commandline
• Commands can be typed directly at the prompt
• To quit type ctrl-d

3
Basic syntax

• Python uses 0 indexing
• Comments
• Lists
• help(list) for more info
• Dictionaries
• help(dict) for more info
• Tuples ()
• help(tuple) for more info

4
Data Types

• Integers x 1
• Floats y 1.0
• x/y will return a float
• Strings string1 text
• You can add text (numbers, lists, etc. must be
  converted into strings before adding)
• string1 \t string2
• string1 str(x)
• string1 .join(list_of_strings)
• Type casting
• int()
• float()
• str()

5
Lists

• list_name
• Similar to an array
• Can contain strings, numbers or both
• Separate elements with commas
• Add new elements with list_name.append()
• Indexing
• list_name0 will return first item
• list_name-1 will return last item
• list_name1-1 will return everything except the
  first and last
• Can create nested lists
• nested a,b,c , 1,2,3 , text
  

6
Dictionaries

• dictionary_name
• Use keys to look up values
• Keys can be text or numbers
• Syntax
• dict 1item1, 2item2
• dict1 will return the text item1
• dict.keys() will return the list 1,2
• dict.vals() will return the list item1,
  item2

7
Tuples

• A tuple is an immutable list
• It cannot be changed. You cant add elements to
  it or remove them from it
• Tuples are faster than lists
• Tuples are secure (write protected)
• Tuples can be used as keys in a dictionary -
  lists cannot

8
Conditional Statements

• ! lt gt gt lt
• if var1 test
• command1
• elif var2 ! test
• command2
• else
• command3
• Test 2 conditions simultaneously using and or
  or

9
Looping

• for, while
• nums 1,2,3
• for j in range(len(nums))
• print j
• -will print 0,1,2
• Can also specify a distinct range to loop over
• for j in range(1,4)
• print j
• -will print 1,2,3

10
Math

• x 2
• y 2
• x y
• xy
• import math
• math.sqrt(xy)
• help(math)

11
Random

• import random
• nums 1,2,3,4,5,6,7,8,9
• random.choice(nums)
• random.sample(nums,4)
• random.shuffle(nums)
• help(random)

12
File I/O

• filehandle file(/path/filename.txt,r)
• text filehandle.readlines()
• filehandle.close()
• Use file or open command
• r - read
• w - write
• a - append
• filehandle.readline() will read one line at a time

13
Parsing Text Files

• f file(/tmp/textfile.txt,r)
• text f.readlines()
• for line in text
• z line.split()
• if z2 CA
• print z0
• f.close()

14
Scripts

• Create a file with a .py extension
• Type the following on the first line
• ! /usr/bin/env python
• Write code and save
• Open a shell. At the commandline
• python filename.py

15
Commandline Arguments

• Use the sys module
• In the code
• import sys
• program_name sys.argv0
• arg1 sys.argv1
• At the command line
• python program_name.py arg1

16
Exceptions

• If you dont want your script to crash on an
  error, you can use try and except
• Syntax
• try
• command
• except
• action to take if command fails
• This is useful for dealing with user input (e.g.
  wrong
• number of command line arguments) and dictionary
• lookup for cases where the key doesnt exist.

17
Getting Help

• gtgtgt help()
• Links on Course Website (Lab page)
• Power Point with basics
• Python tutorial
• Dive Into Python - free online text book

18
Good Coding Practices

• Use self explanatory variable names
• Comment well
• Keep it as simple as possible
• Try to make your programs general (i.e. avoid
  hard coding paths, etc. - use command line
  arguments instead)

19
Basic exercises

• Generate a list of odd numbers between 1 and 1000
  then sum a random subset
• Create a dictionary to convert 3 letter amino
  acid codes to 1 letter amino acid codes
• Parse the pdb file posted on the Lab web page.
  Get the amino acid for each alpha carbon then use
  the dictionary to convert to the 3 letter codes
  into 1 letter codes
• Ex ATOM 2 CA HIS A
• Attempt the exercise posted on the lab website