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

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

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

What is a computer? InputOutput 0 = off 1 = on

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

Where do I get Perl? Course web site for download links and instructions: Windows: ActivePerl MacOS: MacPerl Unix/Linux (FAS): Already Installed

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

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

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

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

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) / ( ); - subtract - multiply - divide natural log

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

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

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

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

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 ) { … } then do this - commands inside curly brackets

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:

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:

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

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

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

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

Two Dimensional Arrays # A 2x2 array of 9 = ([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

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

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

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.

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

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”; Sum of the numbers in data.txt file is 44 chomp command removes “\n” (new line) symbol from the string

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.

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

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

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

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 -- lots of Perl modules use X; - place near the beginning of your program tells Perl to use all the functions in module X

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

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

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

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

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

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

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

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