1. Getting Started with Perl (and Excel) Biophysics 101 September 17, 2003 Griffin Weber (With material from Jon Radoff and Ivan Ovcharenko)

2. What is a computer? Artificial brains? Smarter than you? Too complicated to understand?

3. What is a computer? A machine with lots of buttons The “3 minute popcorn” program: TIME 300 START commands parameter

4. What is a computer? 0110010110101101 InputOutput 0 = off 1 = on

5. What is Perl? Perl is a computer language Easier to use than binary code 01100101print 2+3; Perl Interpreter

6. Where do I get Perl? Course web site for download links and instructions: http://www.courses.fas.harvard.edu/~bphys101/links/index.html Windows: ActivePerl MacOS: MacPerl Unix/Linux (FAS): Already Installed

7. How do you use Perl? Create a new text file Type all the commands Save it as a *.pl file (hello.pl) Tell the computer to run your file perl hello.pl

8. What does Perl look like? #!/usr/local/bin/perl print “Hello everyone\n”; Mandatory first line ! Draw something to the screen

9. Printing Output to the Screen print “Hello \n”; print command: " - place output in quotes \n - end-of-line character (like pressing ‘Enter’) ; - ends every command

10. Variables 2+2 = ? $a = 2; $b = 2; $c = $a + $b; $- indicates a variable ; = - assigns a value to a variable - don’t forget a- the variable name

11. Perl Calculator $c = 4 - 2; $c = 2 * 2; $c = 2 / 2; $c = 2 ** 4;- power : 2^4 2 4 =16 $c = 1.35 * 2 – log(3) / (0.12 + 1); - subtract - multiply - divide natural log

12. Perl Calculator : Output print " 2 + 2 = ". (2+2). "\n"; $c = 2 + 2; print " 2 + 2 = $c \n"; print the value of $c 2 + 2 = 4 or… strings expression concatenate. output

13. Datatypes # DEFINING NUMBERS $x = 4; $x = 1.25; $x = 2.345e-56; # DEFINING STRINGS $x = “ACTGGTA”; $y = “Hello everyone \n”; 2.345 * 10 -56 2.345*10**-56 Perl Examples: # - comment line (Perl ignores)

14. Loops and Cycles : FOR Statement # Output all the numbers from 1 to 100 for ($n=1; $n<=100; $n+=1) { print “$n \n”; } 1. Initialization for ( $n=1 ; $n<=100 ; $n+=1 ) { … } 4. Increment ($n = $n + 1) 2. Termination (stop if this is not true) 3. Body (or block) of the loop - commands inside curly brackets

15. FOR Loop Example Output - Triangle of A’s: for ($line=1; $line<=3; $line+=1) { # output $line ‘A’ symbols for ($n=1; $n<=$line; $n+=1) { print “A”; } # end the line print “\n”; } A AA AAA Source code: Indent = TA

16. Conditional Statements $x = -1; # check whether $x is positive or not if ($x > 0) { print “x = $x is positive\n”; } 1. If this is true,... if ( some_expression ) { … } 2.... then do this - commands inside curly brackets

17. Expressions $x = 1; $y = 2; if ($x < $y) { } if ($x > $y) { } if ($x <= $y) { } if ($x >= $y) { } if ($x == $y) { } if ($x != $y) { } With numbers: Less than Greater than Less than or equal Greater than or equal Equal Not equal $a = “DNA”; $b = “RNA”; if ($a lt $b) { } if ($a gt $b) { } if ($a le $b) { } if ($a ge $b) { } if ($a eq $b) { } if ($a ne $b) { } With strings:

18. Conditional Statements Output: $x = -1; # check whether $x is positive or not if ($x > 0) { print “x = $x is positive\n”; } if ($x < 0) { print “x = $x is negative\n”; } if ($x == 0) { print “x is zero\n”; } x = -1 is negative Source code:

19. Conditional Statements $x = -1; # check whether $x is positive or not if ($x > 0) { print “x = $x is positive\n”; } elsif ($x < 0) { print “x = $x is negative\n”; } else { print “x is zero\n”; } The same thing: if ( some_expression ) { … } else { … } if this is truedo thisotherwisedo this

20. Putting It Together FOR & IF -- all the even numbers from 1 to 100: for ($n=1; $n<=100; $n+=1) { if (($n % 2) == 0) { print “$n”; } Note: $a % $b -- Modulus (remainder when $a is divided by $b) 7 % 2 = 1 5 % 3 = 2 12 % 4 = 0

21. Data Structures : Arrays # array of 5 numbers @a = (7,3,4,-1,0); # array of strings @day = (“Mon”, “Tue”, “Wed”, “Thu”, “Fri”); @- indicates an array(…)- a list of values $a[2]- an element of the array (count from 0)

22. Data Structures : Arrays @a = (7,3,4,-1); # change the value of an element $a[1] = 5; # print all the elements in the array @a for ($i=0; $i<=$#a; $i+=1) { print “a[$i] = $a[$i] \n”; } $#a- the index of the last element in the array @a a[0] = 7 a[1] = 5 a[2] = 4 a[3] = -1

23. Two Dimensional Arrays # A 2x2 array of 9 numbers @a = ([1,2,3],[4,5,6],[7,8,9]); ([…],[…],…,[…])- an array of arrays # change the value of an element $a[1][2] = -1; print “ $a[2][0] \n”; 7

24. Working with Files Microsoft Word Open Edit Save Close Perl Files Open Read or Write (one line at a time) Close

25. Working with Files How to open and close a file “data.txt” from a perl program? # open data.txt file for READING open (FILE, "<data.txt" ); File handler -This name will be used everywhere later in the program, when we will deal with this file. < > Direction of file data flow - READ from a file # close a file specified by FILE file handler close (FILE); - WRITE to a file

26. Working with Files Writing “Hello everyone” to the “tmp.txt” file: #!/usr/local/bin/perl open (FILE, “>tmp.txt”); print FILE “Hello everyone\n”; close (FILE); Note: If tmp.txt already exists, it will be erased.

27. Working with Files # open file data.txt for reading open (FILE, “<data.txt”); # read file line by line and print it out to the screen while ($line = ) { print “$line”; } #close file close(FILE); while loop is analogous to the for loop. All the body statements of it are executed until the condition in parenthesis is false. Read the next line from the file specified by the filehandle

28. Working with Files Example. Calculating a sum of numbers in the file data.txt: #!/usr/local/bin/perl $sum = 0; open (FILE, “<data.txt”); while ($line = ) { chomp($line); $sum = $sum + $line; } close(FILE); print “Sum of the numbers in data.txt file is $sum\n”; 1 18 23 2 Sum of the numbers in data.txt file is 44 chomp command removes “\n” (new line) symbol from the string

29. More Strings $DNA = “ACGTCG”; # length of the string -> number of characters inside $seqLen = length ($DNA); # $seqLen = 6 # extracting a part of a string $seqPart = substr ($DNA, 2, 3); # $seqPart = “GTC” substr ( $string, $offset, $n) -- extracts $n characters from the string $string, starting at the position $offset (first position in a string is 0, not 1!) Note: In Perl, a string is not an array of characters.

30. More Strings $DNA = “ACGTCG”; # length of the string -> number of characters inside $seqRev = reverse ($DNA); # $seqRev = “GCTGCA” # substitute all ‘C’ symbols with ‘T’ symbols $DNA =~ s/C/T/gi; # $DNA = “ATGTTG” s - substitute (search & replace) g – global (everywhere) i – case insensitive # count the number of substitutions $numG = ($DNA =~ s/G//gi); # $numG = 2

31. More Strings $str = “I like biology.”; # replace “biology” with “computers” $str =~ s/biology/computers/; # $str = “I like computers.” # replace ‘r’ with ‘n’, ‘e’ with ‘i’, and ‘s’ with ‘g’ $str =~ tr/res/nig/; # $str = “I liki computing.” Note: tr/// substitutes only symbols, while s/// substitutes strings

32. Functions (Subroutines) $x = min(5,3); print “Smallest of 5 and 3 is: $x\n”; # Function min sub min { ($a, $b) = @_; if ($a < $b) { $small = $a; } else { $small = $b; } return $small; } A function is a program within a program. define the function input parameters return the answer call the function

33. Modules Perl does not have functions for everything, but many useful functions have already programmed by other people, and they share their libraries of functions, which are called modules use bignum; # Work with large numbers use CGI; # Build interactive web pages use BioPerl; # Perform DNA sequence analysis use GD; # Create pictures use DBI; # Communicate with databases http://cpan.org/ -- lots of Perl modules use X; - place near the beginning of your program tells Perl to use all the functions in module X

34. Bugs! $x = 1 if ($x = 1) { $x = 2; } x = 0; $a = (1, 2, 3); $y = 5/$x;

35. Bugs! #!/usr/local/bin/perl $x = 1 if ($x = 1) { $x = 2; } x = 0; $a = (1, 2, 3); $y = 5/$x;

36. Bugs! #!/usr/local/bin/perl $x = 1; if ($x = 1) { $x = 2; } x = 0; $a = (1, 2, 3); $y = 5/$x;

37. Bugs! #!/usr/local/bin/perl $x = 1; if ($x == 1) { $x = 2; } x = 0; $a = (1, 2, 3); $y = 5/$x;

38. Bugs! #!/usr/local/bin/perl $x = 1; if ($x == 1) { $x = 2; } $x = 0; $a = (1, 2, 3); $y = 5/$x;

39. Bugs! #!/usr/local/bin/perl $x = 1; if ($x == 1) { $x = 2; } $x = 0; @a = (1, 2, 3); $y = 5/$x;

40. Bugs! #!/usr/local/bin/perl $x = 1; if ($x == 1) { $x = 2; } $x = 0; @a = (1, 2, 3); $y = 5/$x; # divide by 0

41. Excel What is a worksheet? Enter data by hand Import data from a file Use Excel built-in functions Perform statistical tests Make graphs from data