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Outline

Lab 1 Solution
Program 2
Scoping
Algorithm efficiency
Sorting
Hashes
Review for midterm
Quiz 3

BINF 634 Fall 2013 - LECTURE06

Lab 1 Solution

BINF634 Fall 2013 Regular Expression Lab (Key)

All problems except number 9 are worth 11 points. Number 9 is worth 12 points.

1) Write a PERL regular expression that would match only the strings: “bat”, “at”, and “t”.

/^b?a?t$/

2) Write a PERL regular expression to recognize any string that contains the substring “jeff”.

/jeff/

Lab 1 Solution

3) Write a PERL regular expression that would match the strings: “bat”, “baat”, “baaat”, “baa…aat”, etc. (strings that start with b, followed by one or more a’s, ending with a t).

/^ba+t$/

4) Write a PERL regular expression that matches the strings: “hog”, “Hog”, “hOg”, “HOG”, “hOG”, etc. (That is, “hog” written in any combination of uppercase or lowercase letters.)

/^[hH][oO][Gg]$/

5) Write a PERL regular expression that matches any positive number (with or without a decimal point). Hint #1: if there is a decimal point, there must be at least one digit following the decimal point. Hint #2: Since the dot “.” matches any character, you must use \. to match a decimal point.

/^\d+(\.\d+)?$/

Lab 1 Solution

6) Write a PERL regular expression to match any integer that doesn’t end in 8.

/^\d*[^8]$/

7) Write a PERL regular expression to match any line with exactly two words (or numbers) separated by any amount of whitespace (spaces or tabs). There may or may not be whitespace at the beginning or end of the line.

^\s*\w+\s+\w+\s*$

Program 2 Discussions

Questions on Program 2?
Discussions on the permute function

#!/usr/bin/perl

use strict;

use warnings;

my $x = 23;

print "value in main body is $x \n";

mysub($x);

exit;

sub mysub{

print "value in subroutine is $x \n";

$x=33;

}

value in main body is 23

value in subroutine is 23

#!/usr/bin/perl

use strict;

use warnings;

{

my $x = 23;

mysub($x);

exit;

}

sub mysub{

$x=33;

}

This will not compile

Be Careful With Scope

Scoping

#!/usr/bin/perl

use strict;

use warnings;

{

my $x = 23;

mysub($x);

exit;

}

sub mysub{

my($x) = @_;

$x=33;

}

value in subroutine is 33

Be Careful With Scope (cont.)

Scoping

Data Structures and Algorithm Efficiency

Algorithm Efficiency

Algorithm is O(N2)

# An inefficient way to compute intersections

my @a = qw/ A B C D E F G H I J K X Y Z /;

my @b = qw/ Q R S A C D T U G H V I J K X Z /;

my @intersection = ();

for my $i (@a) {

for my $j (@b) {

if ($i eq $j) {

push @intersection, $i;

last;

}

print "@intersection\n";

exit;

Output:

A C D G H I J K X Z

N = size of Lists

data structures and algorithm efficiency1

Algorithm is O(N)

N = size of Lists

Data Structures and Algorithm Efficiency

# A better way to compute intersections

my @a = qw/ A B C D E F G H I J K X Y Z /;

my @b = qw/ Q R S A C D T U G H V I J K X Z /;

my @intersection = ();

# "mark" each item in @a

my %mark = ();

for my $i (@a) { $mark{$i} = 1 }

# intersection = any "marked" item in @b

for my $j (@b) {

if (exists $mark{$j}) {

push @intersection, $j;

}

print "@intersection\n";

exit;

Output:

A C D G H I J K X Z

version 1

version 2

Demonstration

Unix commands:

/usr/bin/time
head
diff
cmp

% wc -l list1 list2

24762 list1

12381 list2

37143 total

% /usr/bin/time intersect1.pl list1 list2 > out1

22.91 real 22.88 user 0.02 sys

% /usr/bin/time intersect2.pl list1 list2 > out2

0.06 real 0.05 user 0.00 sys

22.88/.05 = 458

Hashes and Efficiency

Hashes

Hashes provide a very fast way to look up information associated with a set of scalar values (keys)
Examples:

Count how many time each word appears in a file

Also: whether or not a certain work appeared in a file

Count how many time each codon appears in a DNA sequence

Whether a given codon appears in a sequence

How many time an item appears in a given list

Intersections

Examples

Hashes

Write a subroutine get_intersection(\@a, \@b) that returns the intersection of two lists.
Write a subroutine first_list_only(\@a, \@b) that returns the items that are in list @a but not in @b.
Write a subroutine unique(@a) that return the unique items in list @a (that is, remove the duplicates).
Write a subroutine dups($n, @a) that returns a list of items that appear in @a at least $n times.

Sorting

sort LIST -- returns list sorted in string order
sort BLOCK LIST -- compares according to BLOCK
sort USERSUB LIST -- compares according subroutine SUB

#!/usr/bin/perl

use strict;

use warnings;

{

my(@unsorted) = (17, 8, 2, 111);

my(@sorted) = sort @unsorted;

print "@unsorted \n";

print "@sorted \n";

exit;

}

Output:

17 8 2 111

111 17 2 8

Sorting Our First Attempt

Sorting

The Comparison Operator

Sorting

1. $a <=> $b returns 0 if equal, 1 if $a > $b, -1 if $a < $b

2. The "cmp" operator gives similar results for strings

3. $a and $b are special global variables:

do NOT declare with "my" and do NOT modify.

#!/usr/bin/perl

use strict;

use warnings;

{

my(@unsorted) = (17, 8, 2, 111);

my(@sorted) = sort { $a <=> $b }@unsorted;

print "@sorted \n";

exit;

}

Output:

17 8 2 111

2 8 17 111

Sorting Numerically

Sorting

#!/usr/bin/perl

use strict;

use warnings;

{

my(@unsorted) = (17, 8, 2, 111);

my(@sorted) = sort numerically @unsorted;

print "@sorted \n";

exit;

}

sub numerically { $a <=> $b }

Output:

17 8 2 111

2 8 17 111

Sorting Using a Subroutine

Sorting

#!/usr/bin/perl

use strict;

use warnings;

{

my(@unsorted) = (17, 8, 2, 111);

my(@reversesorted) = reverse sort numerically @unsorted;

print "@reversesorted \n";

exit;

}

sub numerically { $a <=> $b }

Output:

17 8 2 111

111 17 8 2

Sorting Descending

Sorting

!/usr/bin/perl

use strict;

use warnings;

{

# Sorting strings:

my @dna = qw/ TATAATG TTTT GT CTCAT /;

## Sort @dna by length:

@dna = sort { length($a) <=> length($b) }@dna;

print "@dna\n"; # Output: GT TTTT CTCAT TATAATG

exit;

}

Output:

GT TTTT CTCAT TATAATG

Sorting DNA by Length

Sorting

#!/usr/bin/perl

use strict;

use warnings;

{

# Sorting strings:

@dna = sort { ($b =~ tr/Tt//) <=> ($a =~ tr/Tt//) } @dna;

print "@dna\n"; # Output: TTTT TATAATG CTCAT GT

exit;

}

Output:

TTTT TATAATG CTCAT GT

Sorting DNA by Number of T’s (Largest First)

Sorting

#!/usr/bin/perl

use strict;

use warnings;

{

# Sorting strings:

@dna = reverse sort {

($a =~ tr/Tt//) <=> ($b =~ tr/Tt//) } @dna;

print "@dna\n"; # Output: TTTT TATAATG CTCAT GT

exit;

}

Output:

TTTT TATAATG CTCAT GT

Sorting DNA by Number of T’s (Largest First) (Take 2)

Sorting

#!/usr/bin/perl

use strict;

use warnings;

{

# Sort strings without regard to case:

my(@unsorted) = qw/ mouse Rat HUMAN eColi /;

my(@sorted) = sort { lc($a) cmp lc($b) } @unsorted;

print "@sorted \n";

exit;

}

Output:

mouse Rat HUMAN eColi

eColi HUMAN mouse Rat

Sorting Strings Without Regard to Case

Sorting

#!/usr/bin/perl

use strict;

use warnings;

{

my(%sales_amount) = ( auto=>100, kitchen=>2000, hardware=>200 );

sub bysales { $sales_amount{$b} <=> $sales_amount{$a} }

for my $dept (sort bysales keys %sales_amount) {

printf "%s:\t%4d\n", $dept, $sales_amount{$dept};

}

exit;

}

Output:

kitchen:2000

hardware: 200

auto: 100

Sorting Hashes by Value

Sorting

Review for Midterm BINF634

Midterm

Material

Tisdall Chapters 1-9
Wall Chapter 5
Lecture notes

The exam will be open book and notes
You cannot work together on it
You cannot use outside material
You will have the full period to take the midterm
You will be asked to program

Some Example Questions

Midterm

Given two DNA fragments contained in $DNA1 and $DNA2 how can we concatenate these to make a third string $DNA3?

Midterm

What does this line of code do?

$RNA = ~ s/T/U/ig

Midterm

What does this statement do?

$revcom =~ tr/ACGT/TGCA/;

Midterm

What do these four lines do?

@bases = (‘A’, ‘C’, ‘G’, ‘T’);

$base1 = pop @bases;

unshift (@bases, $base1);

print “@bases\n\n”;

Midterm

What does this code snippet do if COND is true

unless(COND){

#do something

}

Midterm

What does this code fragment do?

$protein = join(‘’,@protein)

Midterm

$myfile = “myfile”;

Open(MYFILE, “>$myfile”)

Midterm

while($DNA =~ /a/ig){$a++}

Midterm

What is the effect of using the command

use strict;

at the beginning of your program?

Midterm

What is contained in the reserved variable $0 and

in the array @ARGV ?

Midterm

What is the difference between “pass by value” and “pass by reference” ?

Midterm

What is a pointer and what does it mean to dereference a pointer?

Midterm

How do you invoke perl with the debugger?

Midterm

Given an array @verbs what is going on here?

$verbs[rand @verbs]

For the Curious Regarding Data Structures and Their Implications

Niklaus Wirth, Algorithms + Data Structures = Programs, Prentice Hall 1976.

Dated in terms of language, Pascal, but very well written and understandable

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