Class 2

Send programs and assignments to
gogarten@uconn.edu

Grades: based on homework assignments

Check for problems (compare class 1):

• ssh?
• connecting to biotech cluster?
• basic unix commands?
• vi?
• vi and color?
  One problem is that in the ssh program under windows, the ANSI setting of the ssh program produces black error messages on a dark black background. So far I have not found a good solution. There are two workarounds: look very closely at the black box that pops up, if you do something "wrong" in vi; or set the foreground color to dark gray. (gray on dark blue is sill readable).
• basic vi commands?
• which PERL?
• End of line problems?

To run PERL script:

perl myprogram.pl

In unix
   chmod 755 *.pl
or
   chmod a+x *.pl
turns the files with extension into pl into executables. Then
   ./myprogram.pl
executes the program.

DON'T RUN THINGS ON THE MASTER NODE ! (At least not things that take longer than a second)

qrsh

or
ssh node010

Check notes for class1 regarding student projects

Old Assignments:

• Read handouts on variables, <>, and chomp
• Read the above
• Install ssh on your computer
• log into your account at bbcxsrv1.biotech.uconn.edu
  (if you use ssh under windows go to the "profile" menu, add a profile, THEN edit the profile, THEN use the profile - this is somewhat backwards, but it works, in the future you only need to select the profile)
• Once you logged in change your password. To do so type he command passwd <return>
• start the vi editor and create a .vimrc file that allows you to use context dependent colors (see above)
• ex1.1: Create first Perl Program- “hello, world!” [make file executable using chmod 755 *.pl]
  #!/usr/bin/perl -w
  print ("Hello, world!\n");
  What does the -w stand for? What happens if you leave out the new line character?
  You can run the program by typing ./program_name.pl, if the file containing the program is an executable.
• ex1.2 modify the program so that it asks for your name and then greets you by a phrase like "hello $your_name.
• ex2.1: Write a program that computes the circumference of a circle with a radius of 12.5. The circumference is 2[pi] times the radius, or about 2 times 3.141592654 times the radius.
• ex2.2: Modify the program from the previous exercise to prompt for and accept a radius from the person running the program.
• Email the programs as separate attachments to gogarten@uconn.edu (i.e. one email, with several independent files as attachments).
  

Name the attachments so that they have .pl as extension (then my mail program reconizes them as perl scripts and I can execute them directly in a terminal window).
Don't use last year's sample programs as a study guide!
Don't give up on use strict -- missing ";" are easy to identify, but keeping track of variables created somewhere along a line is more difficult.
Sample Programs are at ex1-1, ex1-3, ex2-1, ex 2-2, ex2-2mod, ex2-3
Discuss modules
New things - annotated example

Numerical Operators:

Operator	Associativity	Description
**	right	exponentiation
*, /, %	left	multiplication, division, modulus
+, -	left	addition, subtraction
+=,-=,*=
++,--	none	autoincrement/decrement

Examples

my $x = 5 * 2 + 3; # $x is 13
my $y = 2 * $x / 4; # $y is 6.5
my $z = (2 ** 6) ** 2; # $z is 4096
my $a = ($z - 96) * 2; # $a is 8000
my $b = $x % 5; # 3, 13 modulo 5
my $d = $b++; #$b is 4, $d is 3
$d = ++$b; #$b and $d are both 5

Script is here

Binary Assignment Operators
(=     **=     +=     *=      .= )
(if you want to ask is something equal to, you need to use == see below)

my $a = $a + 5; # without the binary assignment operator
$a += 5; # with the binary assignment operator

my $b = $b * 3; # without the binary assignment operator
$b *= 3; # with the binary assignment operator

my $str
$str = $str . " "; # append a space to $str
$str .= " 1"; # same thing with assignment operator

$a = 3;
$b = ($a += 4); # $a and $b are both now 7

$a=2;
$a **= 3; # with the binary assignment operator
$a=2;
$a = $a** 3;# withou the binary assignment operator

Script here

Numeric and String Comparison Operators:

logical AND in perl: &&
logical or in perl: ||

New Assignments:

• A) What is the value of $i after each step of the following script
  
  $i = 1;
  $i++;
  $i *= $i;
  $i .= $i;
  $i=$i/11;
  $i=$i . "score and" . $i+3 ;
  $i=$i +3 . "score and" . $i ;

• B) Write a script that tests your answers for A - explain any discrepancies.

• C) If $a =1 and $b = 2, what is the type and value of the scalar stored in $c after each statement?
  (you might need to turn the warnings off to force the code to execute)
  
  $c = $a +$b;
  $c = $a / $b;
  $c = "$a + $b";
  $c = '$a + $b';
  $c = $a + $b++;
  $c += $a

• D) Write a script that tests your answers for C - explain any discrepancies.

E) For the following array declaration

@myArray = ('A', 'B', 'C', 'D', 'E');

what is the value of the following expressions:

$#myArray
length(@myArray)
$myArray[1]
$n=@myArray
reverse (@myArray)
 

• F) Add all numbers between 1 and 50 using the following control structures
  while () {};
  (while ($n<50){print "$n\n"; $n +=2;} where ($n<50) is the condition and {print "$n\n"; $n +=2;} is what is being done while the condition is true.
  for () {};
  (for ($i=0; $i<51; $i += 1) {print "$i"}where $i=0 is the initialization, $i<51 is the test and $i += 1 is the increment and {print "$i"}is what is being done.)
  foreach () {}; # you first need to assign the numbers 1 through 50 to an array. An easy way to do this is to use the following assignment:
  @numbers = (1..50);
  (foreach $n (@numbers) {$sum+=$n;} where $n is the name of the variable that is successivly assigned the values form the list (@numbers). If $n is not specified, the variable is $_ (see here for emaple)
   
• G) Do the following statements evaluate true or false?
  a) 1
  b) 0&&1
  c) 0||1
  d) 45
  e) 45-45
  f) 45/45
  g) 45==45
  h) $a=45
  i) 45 <=> 45
  An example for the if () {}else {} is here (Note: no ; between {} else {})
   
• READ HANDOUT