Introduction to Python

Chen Lin
clin@brandeis.edu
COSI 134a
Volen 110
Office Hour: Thurs. 3-5

For More Information?

http://python.org/
- documentation, tutorials, beginners guide, core
distribution, ...
Books include:
Learning Python by Mark Lutz
Python Essential Reference by David Beazley
Python Cookbook, ed. by Martelli, Ravenscroft and
Ascher
(online at
http://code.activestate.com/recipes/langs/python/)
http://wiki.python.org/moin/PythonBooks

Python Videos
http://showmedo.com/videotutorials/python
5 Minute Overview (What Does Python
Look Like?)
Introducing the PyDev IDE for Eclipse
Linear Algebra with Numpy
And many more

4 Major Versions of Python

Python

or CPython is written in C/C++

- Version 2.7 came out in mid-2010
- Version 3.1.2 came out in early 2010

Jython

is written in Java for the JVM

IronPython is written in C# for the .Net
environment
Go To Website

Development Environments
what IDE to use? http://stackoverflow.com/questions/81584

1. PyDev with Eclipse

2. Komodo
3. Emacs
4. Vim
5. TextMate
6. Gedit
7. Idle
8. PIDA (Linux)(VIM Based)
9. NotePad++ (Windows)
10.BlueFish (Linux)

Pydev with Eclipse

Python Interactive Shell

% python
Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
You can type things directly into a running Python session
>>> 2+3*4
14
>>> name = "Andrew"
>>> name
'Andrew'
>>> print "Hello", name
Hello Andrew
>>>

 Background
Data Types/Structure
Control
File

flow

I/O
Modules
Class
NLTK

List
A compound data type:
[0]
[2.3, 4.5]
[5, "Hello", "there", 9.8]
[]
Use len() to get the length of a list
>>> names = [Ben", Chen", Yaqin"]
>>> len(names)
3

Use [ ] to index items in the list

>>> names[0]
Ben'
>>> names[1]
Chen'
>>> names[2]
Yaqin'
>>> names[3]
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
IndexError: list index out of range
>>> names[-1]
Yaqin'
>>> names[-2]
Chen'
>>> names[-3]
Ben'

[0] is the first item.

[1] is the second item
...
Out of range values
raise an exception
Negative values
go backwards from
the last element.

Strings share many features with lists

>>> smiles = "C(=N)(N)N.C(=O)(O)O"
>>> smiles[0]
'C'
>>> smiles[1]
'('
>>> smiles[-1]
Use slice notation to
'O'
get a substring
>>> smiles[1:5]
'(=N)'
>>> smiles[10:-4]
'C(=O)'

String Methods: find, split

smiles = "C(=N)(N)N.C(=O)(O)O"
>>> smiles.find("(O)")
15
Use find to find the
start of a substring.
>>> smiles.find(".")
9
Start looking at position 10.
>>> smiles.find(".", 10)
Find returns -1 if it couldnt
-1
find a match.
>>> smiles.split(".")
Split the string into parts
['C(=N)(N)N', 'C(=O)(O)O'] with . as the delimiter
>>>

String operators: in, not in

if "Br" in Brother:
print "contains brother
email_address = clin
if "@" not in email_address:
email_address += "@brandeis.edu

String Method: strip, rstrip, lstrip are ways to

remove whitespace or selected characters
>>> line = " # This is a comment line \n"
>>> line.strip()
'# This is a comment line'
>>> line.rstrip()
' # This is a comment line'
>>> line.rstrip("\n")
' # This is a comment line '
>>>

More String methods

email.startswith(c") endswith(u)
True/False
>>> "%s@brandeis.edu" % "clin"
'clin@brandeis.edu'
>>> names = [Ben", Chen", Yaqin"]
>>> ", ".join(names)
Ben, Chen, Yaqin
>>> chen".upper()
CHEN'

Unexpected things about strings

>>> s = "andrew"
Strings are read only
>>> s[0] = "A"
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: 'str' object does not support item
assignment
>>> s = "A" + s[1:]
>>> s
'Andrew

\ is for special characters

\n -> newline
\t -> tab
\\ -> backslash
...
But Windows uses backslash for directories!
filename = "M:\nickel_project\reactive.smi" # DANGER!
filename = "M:\\nickel_project\\reactive.smi" # Better!
filename = "M:/nickel_project/reactive.smi" # Usually works

Lists are mutable - some useful

methods
append an element

>>> ids = ["9pti", "2plv", "1crn"]

>>> ids.append("1alm")
>>> ids
['9pti', '2plv', '1crn', '1alm']
>>>ids.extend(L)
Extend the list by appending all the items in the given list; equivalent to a[len(a):] = L.
>>> del ids[0]
>>> ids
['2plv', '1crn', '1alm']
>>> ids.sort()
>>> ids
['1alm', '1crn', '2plv']
>>> ids.reverse()
>>> ids
['2plv', '1crn', '1alm']
>>> ids.insert(0, "9pti")
>>> ids
['9pti', '2plv', '1crn', '1alm']

remove an element

sort by default order

reverse the elements in a list

insert an element at some
specified position.
(Slower than .append())

Tuples: sort of an immutable list

>>> yellow = (255, 255, 0) # r, g, b
>>> one = (1,)
>>> yellow[0]
>>> yellow[1:]
(255, 0)
>>> yellow[0] = 0
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: 'tuple' object does not support item assignment

Very common in string interpolation:

>>> "%s lives in %s at latitude %.1f" % ("Andrew", "Sweden", 57.7056)
'Andrew lives in Sweden at latitude 57.7'

zipping lists together

>>> names
['ben', 'chen', 'yaqin']
>>> gender = [0, 0, 1]
>>> zip(names, gender)
[('ben', 0), ('chen', 0), ('yaqin', 1)]

Dictionaries

Dictionaries are lookup tables.

They map from a key to a value.
symbol_to_name = {
"H": "hydrogen",
"He": "helium",
"Li": "lithium",
"C": "carbon",
"O": "oxygen",
"N": "nitrogen"
}

Duplicate

keys are not allowed

Duplicate values are just fine

Keys can be any immutable value

numbers, strings, tuples, frozenset ,
not list, dictionary, set, ...

atomic_number_to_name = { A set is an unordered collection

1: "hydrogen"
with no duplicate elements.
6: "carbon",
7: "nitrogen"
8: "oxygen",
}
nobel_prize_winners = {
(1979, "physics"): ["Glashow", "Salam", "Weinberg"],
(1962, "chemistry"): ["Hodgkin"],
(1984, "biology"): ["McClintock"],
}

Dictionary

Get the value for a given key

>>> symbol_to_name["C"]
'carbon'
>>> "O" in symbol_to_name, "U" in symbol_to_name
(True, False)
Test if the key exists
>>> "oxygen" in symbol_to_name
(in only checks the keys,
False
not the values.)
>>> symbol_to_name["P"]
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
KeyError: 'P'
>>> symbol_to_name.get("P", "unknown")
'unknown'
>>> symbol_to_name.get("C", "unknown")
[] lookup failures raise an exception.
'carbon'
Use .get() if you want
to return a default value.

Some useful dictionary methods

>>> symbol_to_name.keys()
['C', 'H', 'O', 'N', 'Li', 'He']
>>> symbol_to_name.values()
['carbon', 'hydrogen', 'oxygen', 'nitrogen', 'lithium', 'helium']
>>> symbol_to_name.update( {"P": "phosphorous", "S": "sulfur"} )
>>> symbol_to_name.items()
[('C', 'carbon'), ('H', 'hydrogen'), ('O', 'oxygen'), ('N', 'nitrogen'), ('P',
'phosphorous'), ('S', 'sulfur'), ('Li', 'lithium'), ('He', 'helium')]
>>> del symbol_to_name['C']
>>> symbol_to_name
{'H': 'hydrogen', 'O': 'oxygen', 'N': 'nitrogen', 'Li': 'lithium', 'He': 'helium'}

 Background
Data Types/Structure

list, string, tuple, dictionary

Control flow
File I/O
Modules
Class
NLTK

Control Flow
Things that are False
The boolean value False
The numbers 0 (integer), 0.0 (float) and 0j (complex).
The empty string "".
The empty list [], empty dictionary {} and empty set set().
Things that are True
The boolean value True
All non-zero numbers.
Any string containing at least one character.
A non-empty data structure.

If
>>> smiles = "BrC1=CC=C(C=C1)NN.Cl"
>>> bool(smiles)
True
>>> not bool(smiles)
False
>>> if not smiles:
...
print "The SMILES string is empty"
...
The else case is always optional

Use elif to chain subsequent tests

>>> mode = "absolute"
>>> if mode == "canonical":
... smiles = "canonical"
... elif mode == "isomeric":
... smiles = "isomeric
... elif mode == "absolute":
... smiles = "absolute"
... else:
... raise TypeError("unknown mode")
...
>>> smiles
' absolute '
>>>

raise is the Python way to raise exceptions

Boolean logic
Python expressions can have ands and
ors:
if (ben <= 5 and chen >= 10 or
chen == 500 and ben != 5):
print Ben and Chen

Range Test
if (3 <= Time <= 5):
print Office Hour"

For
>>> names = [Ben", Chen", Yaqin"]
>>> for name in names:
...
print smiles
...
Ben
Chen
Yaqin

Tuple assignment in for loops

data = [ ("C20H20O3", 308.371),
("C22H20O2", 316.393),
("C24H40N4O2", 416.6),
("C14H25N5O3", 311.38),
("C15H20O2", 232.3181)]
for (formula, mw) in data:
print "The molecular weight of %s is %s" % (formula, mw)
The molecular weight of C20H20O3 is 308.371
The molecular weight of C22H20O2 is 316.393
The molecular weight of C24H40N4O2 is 416.6
The molecular weight of C14H25N5O3 is 311.38
The molecular weight of C15H20O2 is 232.3181

Break, continue
>>>
...
...
...
...
...
...
...
...
...

Checking 3
for value in [3, 1, 4, 1, 5, 9, 2]:
The square is 9
Checking 1
print "Checking", value
Ignoring
if value > 8:
Checking 4
The square is 16
print "Exiting for loop"
Use breakChecking
to stop 1
break
the for loopIgnoring
Checking 5
elif value < 3:
The to
square
Use continue
stop is 25
print "Ignoring"
processing Checking
the current9 item
Exiting for loop
continue
>>>

print "The square is", value**2

Range()

range creates a list of numbers in a specified range

range([start,] stop[, step]) -> list of integers
When step is given, it specifies the increment (or decrement).

>>> range(5)
[0, 1, 2, 3, 4]
>>> range(5, 10)
[5, 6, 7, 8, 9]
>>> range(0, 10, 2)
[0, 2, 4, 6, 8]

How to get every second element in a list?

for i in range(0, len(data), 2):
print data[i]

 Background
Data Types/Structure
Control
File

flow

I/O
Modules
Class
NLTK

Reading files
>>> f = open(names.txt")
>>> f.readline()
'Yaqin\n'

Quick Way
>>> lst= [ x for x in open("text.txt","r").readlines() ]
>>> lst
['Chen Lin\n', 'clin@brandeis.edu\n', 'Volen 110\n', 'Office
Hour: Thurs. 3-5\n', '\n', 'Yaqin Yang\n',
'yaqin@brandeis.edu\n', 'Volen 110\n', 'Offiche Hour:
Tues. 3-5\n']

Ignore the header?

for (i,line) in enumerate(open(text.txt,"r").readlines()):
if i == 0: continue
print line

Using dictionaries to count

occurrences
>>> for line in open('names.txt'):
...
name = line.strip()
...
name_count[name] = name_count.get(name,0)+ 1
...
>>> for (name, count) in name_count.items():
...
print name, count
...
Chen 3
Ben 3
Yaqin 3

File Output
input_file = open(in.txt")
output_file = open(out.txt", "w")
for line in input_file:
w = write mode
output_file.write(line) a = append mode
wb = write in binary
r = read mode (default)
rb = read in binary
U = read files with Unix
or Windows line endings

 Background
Data Types/Structure
Control
File

flow

I/O
Modules
Class
NLTK

Modules
When

a Python program starts it only has

access to a basic functions and classes.
(int, dict, len, sum, range, ...)
Modules contain additional functionality.
Use import to tell Python to load a
module.
>>> import math
>>> import nltk

import the math module

>>> import math
>>> math.pi
3.1415926535897931
>>> math.cos(0)
1.0
>>> math.cos(math.pi)
-1.0
>>> dir(math)
['__doc__', '__file__', '__name__', '__package__', 'acos', 'acosh',
'asin', 'asinh', 'atan', 'atan2', 'atanh', 'ceil', 'copysign', 'cos',
'cosh', 'degrees', 'e', 'exp', 'fabs', 'factorial', 'floor', 'fmod',
'frexp', 'fsum', 'hypot', 'isinf', 'isnan', 'ldexp', 'log', 'log10',
'log1p', 'modf', 'pi', 'pow', 'radians', 'sin', 'sinh', 'sqrt', 'tan',
'tanh', 'trunc']
>>> help(math)
>>> help(math.cos)

import and from ... import ...

>>> import math
math.cos
>>> from math import cos, pi
cos
>>> from math import *

 Background
Data Types/Structure
Control
File

flow

I/O
Modules
Class
NLTK

Classes
class ClassName(object):
<statement-1>
...
<statement-N>
class MyClass(object):
"""A simple example class"""
i = 12345
def f(self):
return self.i
class DerivedClassName(BaseClassName):
<statement-1>
...
<statement-N>

 Background
Data Types/Structure
Control
File

flow

I/O
Modules
Class
NLTK

http://www.nltk.org/book
NLTK is on berry patch machines!
>>>from nltk.book import *
>>> text1
<Text: Moby Dick by Herman Melville 1851>
>>> text1.name
'Moby Dick by Herman Melville 1851'
>>> text1.concordance("monstrous")
>>> dir(text1)
>>> text1.tokens
>>> text1.index("my")
4647
>>> sent2
['The', 'family', 'of', 'Dashwood', 'had', 'long', 'been', 'settled', 'in',
'Sussex', '.']

Classify Text
>>> def gender_features(word):
...
return {'last_letter': word[-1]}
>>> gender_features('Shrek')
{'last_letter': 'k'}
>>> from nltk.corpus import names
>>> import random
>>> names = ([(name, 'male') for name in names.words('male.txt')] +
... [(name, 'female') for name in names.words('female.txt')])

>>> random.shuffle(names)

Featurize, train, test, predict

>>> featuresets = [(gender_features(n), g) for (n,g) in names]
>>> train_set, test_set = featuresets[500:], featuresets[:500]
>>> classifier = nltk.NaiveBayesClassifier.train(train_set)
>>> print nltk.classify.accuracy(classifier, test_set)
0.726
>>> classifier.classify(gender_features('Neo'))
'male'

from nltk.corpus import reuters

Reuters

Corpus:10,788 news
1.3 million words.
Been classified into 90 topics
Grouped into 2 sets, "training" and "test
Categories overlap with each other
http://nltk.googlecode.com/svn/trunk/doc/bo
ok/ch02.html

Reuters
>>> from nltk.corpus import reuters
>>> reuters.fileids()
['test/14826', 'test/14828', 'test/14829', 'test/14832', ...]

>>> reuters.categories()
['acq', 'alum', 'barley', 'bop', 'carcass', 'castor-oil', 'cocoa', 'coconut',
'coconut-oil', 'coffee', 'copper', 'copra-cake', 'corn', 'cotton', 'cottonoil', 'cpi', 'cpu', 'crude', 'dfl', 'dlr', ...]