An Introduction to Python Part III

1
An Introduction to Python Part III

• Dr. Nancy Warter-Perez

2
Overview

• Assignments
• Solution to Programming Workshop 2
• 2-D Lists
• List comprehensions
• Zip
• File I/O
• Split
• Functions
• Programming Workshop 3

3
Solution to Programming Workshop 2

• Script to calculate GC of a sequence of
  nucleotides.
• Inputs sequence, window size
• Outputs nucleotide number, GC for each window
• Written by Nancy Warter-Perez
• Date created April 22, 2004
• Last modified
• print("Script for computing GC.")
• seq raw_input("Please enter sequence ")
• winsize input("Please enter window size ")

4
Solution to Programming Workshop 2
print("nucleotide\tGC") for i in range(0,
len(seq)-winsize1) cnt0 for j in
seqiiwinsize if(j'G' or j'C' or
j'g' or j 'c') cnt1 gc
(cnt100.0)/winsize print"i\t\t.2f"
((i1winsize/2),gc) x raw_input("\n\nPlease
enter any character to exit.\n")
5
Python List Comprehensions

• Precise way to create a list
• Consists of an expression followed by a for
  clause, then zero or more for or if clauses
• Ex
• gtgtgt 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
• gtgtgt x "acactgacct"
• gtgtgt y int(i'c' or i'g') for i in x
• gtgtgt y
• 0, 1, 0, 1, 0, 1, 0, 1, 1, 0

6
Creating 2-D Lists

• 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)
• To assign the value 5 to the element at the 2nd
  row and 3rd column of L
• L23 5

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Zip for parallel traversals

• Visit multiple sequences in parallel
• Ex
• gtgtgt L1 1,2,3
• gtgtgt L2 5,6,7
• gtgtgt zip(L1, L2)
• (1,5), (2,6), (3,7)
• Ex
• gtgtgt for(x,y) in zip(L1, L2)
• print x, y, '--', xy
• 1 5 -- 6
• 2 6 -- 8
• 3 7 -- 10

8
More on Zip

• Zip more than two arguments and any type of
  sequence
• Ex
• gtgtgt T1, T2, T3 (1,2,3),(4,5,6),(7,8)
• gtgtgt T3
• (7,8)
• gtgtgt zip(T1, T2, T3)
• (1,4,7),(2,5,8) -- truncates to shortest
  sequence

9
Dictionary Construction with zip

• Ex
• gtgtgt keys 'a', 'b', 'd'
• gtgtgt vals 1.8, 2.5, -3.5
• gtgtgt hydro dict(zip(keys,vals))
• gtgtgt hydro
• 'a' 1.8, 'b' 2.5, 'd' -3.5

10
File I/O

• To open a file
• myfile open('pathname', ltmodegt)
• 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
12
Common output file operations
13
Extracting data from string split

• 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 maxsplit1 elements).

14
Split

• Ex
• gtgtgt x "a,b,c,d"
• gtgtgt x.split(',')'a', 'b', 'c', 'd'
• gtgtgt x.split(',',2)'a', 'b', 'c,d'
• Ex
• gtgtgt y "5 33 a 4"
• gtgtgt y.split()'5', '33', 'a', '4'

15
Functions

• Function definition
• def adder(a, b, c) return abc
• Function calls
• adder(1, 2, 3) -gt 6

16
Functions Polymorphism

• gtgtgtdef fn2(c)
• a c 3
• return a
• gtgtgt print fn2(5)
• 15
• gtgtgt print fn2(1.5)
• 4.5
• gtgtgt print fn2(1,2,3)
• 1,2,3,1,2,3,1,2,3
• gtgtgt print fn2("Hi")
• HiHiHi

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Functions - Recursion

• def fn_Rec(x)
• if x
• return
• fn_Rec(x1)
• print x0,
• y 1,2,3,4
• fn_Rec(y)
• gtgtgt 4 3 2 1

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Programming Workshop 3

• Create a text file called "test1.txt" with the
  following data
• Sample data
• 1 2 3 4 5
• more data
• 6 7 8 9 10
• Create another text filed called "test2.txt" with
  the following data
• More test data
• With more header info
• A B C D E F G
• Write a script to do the following
• 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

• 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, May 14th

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Example Scoring Matrix File
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Algorithm for Homework 2P

• 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 doesnt 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
• 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 youve read all lines, create the
  dictionary of dictionaries by zipping the keys
  and the list of dictionaries and convert into a
  dictionary.