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An Introduction to Python – Part III
Dr. Nancy Warter-Perez
Overview
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2-D Lists
List comprehensions
Zip
File I/O
Split
Functions
Programming Workshop #3
Introduction to Python – Part III
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Python List Comprehensions
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Precise way to create a list
Consists of an expression followed by a for clause,
then zero or more for or if clauses
Ex:
>>> [str(round(355/113.0, i)) for i in range(1,6)] ['3.1',
'3.14', '3.142', '3.1416', '3.14159']
Ex: replace all occurrences of G or C in a string of
amino acids with a 1 and A and T with a 0
>>> x = "acactgacct"
>>> y = [int(i=='c' or i=='g') for i in x]
>>> y
[0, 1, 0, 1, 0, 1, 0, 1, 1, 0]
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Creating 2-D Lists
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To create a 2-D list L, with C columns and R
rows initialized to 0:
L = [[]] #empty 2-Dlist
L = [[0 for col in range(C)] for row in range(R)]
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To assign the value 5 to the element at the
2nd row and 3rd column of L
L[2][3] = 5
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Zip – for parallel traversals
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Visit multiple sequences in parallel
Ex:
>>> L1 = [1,2,3]
>>> L2 = [5,6,7]
>>> zip(L1, L2)
[(1,5), (2,6), (3,7)]
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Ex:
>>> for(x,y) in zip(L1, L2):
…
print x, y, '--', x+y
1 5 -- 6
2 6 -- 8
3 7 -- 10
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More on Zip
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Zip more than two arguments and any
type of sequence
Ex:
>>> T1, T2, T3 = (1,2,3),(4,5,6),(7,8)
>>> T3
(7,8)
>>> zip(T1, T2, T3)
[(1,4,7),(2,5,8)] -- truncates to shortest sequence
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Dictionary Construction with
zip
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Ex:
>>> keys = ['a', 'b', 'd']
>>> vals = [1.8, 2.5, -3.5]
>>> hydro = dict(zip(keys,vals))
>>> hydro
{'a': 1.8, 'b': 2.5, 'd': -3.5}
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File I/O
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To open a file
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myfile = open('pathname', <mode>)
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modes:
'r' = read
'w' = write
Ex: infile = open("D:\\Docs\\test.txt", 'r')
Ex: outfile = open("out.txt", 'w') – in same
directory
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Common input file operations
Operation
input = open ('file', 'r')
S = input.read()
S = input.read(N)
S = input.readline()
L = input.readlines()
Interpretation
open input file
read entire file into
string S
Read N bytes (N>= 1)
Read next line
Read entire file into list
of line strings
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Common output file operations
Operation
Interpretation
output = open('file', 'w') create output file
output.write(S)
Write string S into file
output.writelines(L)
Write all line strings in
list L into file
output.close()
Manual close (good
habit)
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Extracting data from string –
split
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String.split([sep, [maxsplit]]) - Return a list of the words
of the string s.
If the optional argument sep is absent or None, the
words are separated by arbitrary strings of whitespace
characters (space, tab, newline, return, formfeed).
If the argument sep is present and not None, it specifies
a string to be used as the word separator.
The optional argument maxsplit defaults to 0. If it is
nonzero, at most maxsplit number of splits occur, and
the remainder of the string is returned as the final
element of the list (thus, the list will have at most
maxsplit+1 elements).
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Split
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Ex:
>>> x = "a,b,c,d"
>>> x.split(',')['a', 'b', 'c', 'd']
>>> x.split(',',2)['a', 'b', 'c,d']
 Ex:
>>> y = "5
33 a
4"
>>> y.split()['5', '33', 'a', '4']
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Functions
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Function definition
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def adder(a, b, c): return a+b+c
Function calls
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adder(1, 2, 3) -> 6
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Functions – Polymorphism
>>>def fn2(c):
…
a=c*3
…
return a
>>> print fn2(5)
15
>>> print fn2(1.5)
4.5
>>> print fn2([1,2,3])
[1,2,3,1,2,3,1,2,3]
>>> print fn2("Hi")
HiHiHi
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Functions - Recursion
def fn_Rec(x):
if x == []:
return
fn_Rec(x[1:])
print x[0],
y = [1,2,3,4]
fn_Rec(y)
>>> 4 3 2 1
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Programming Workshop #3
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Create a text file called "test1.txt" with the following data:
# Sample data
12345
# more data
6 7 8 9 10
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Create another text filed called "test2.txt" with the following data:
# More test data
# With more header info
ABCDEFG
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Write a script to do the following
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1. Prompt the user for a filename
2. Open the file
3. Read the file into a list of strings.
4. If the line does not begin with a '#' print the line to the screen.
Test your script on test1.txt and test2.txt.
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Programming Homework #2P
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Write a program to prompt the user for a
scoring matrix file name and read the data
into a dictionary
Download a representative set of PAM and
Blossum Scoring Matrix Files
Scoring matrices should be downloaded from
ftp://ftp.ncbi.nih.gov/blast/matrices/
Due Date: Thursday, November 8th (must
submit to get an extension)
One Week Automatic Extension: Thursday,
November 15th
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Example Scoring Matrix File
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Algorithm for Homework 2P
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Step 1: Create an empty list (of dictionaries)
Step 2: Prompt the user for the scoring matrix file name
Step 3: Open the file and read the contents as a list of strings.
Ignore the comment lines
Step 4: When you reach a line that doesn’t start with '#' read in the
amino acid symbols and split them into your keys for your dictionary
Step 5: Read in the rest of the lines one at a time. For each line:
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Step 5a. Slice off the first character (amino acid).
Step 5b. For the rest of the string split into individual numbers and
convert to a list of integers (use a list comprehension). This is your data
for your dictionary.
Step 5c. Zip the keys and data together and convert into a dictionary.
Step 5d. Add the dictionary to the list of dictionaries
Step 6: After you’ve read all lines, create the dictionary of dictionaries
by zipping the keys and the list of dictionaries and convert into a
dictionary.
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