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Getting Started with Perl (and Excel)

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

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Getting Started with Perl (and Excel)

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  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: parameter TIME 300 START commands

  4. What is a computer? Input Output 01100101 10101101 0 = off 1 = on

  5. What is Perl? • Perl is a computer language • Easier to use than binary code Perl print 2+3; 01100101 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? Mandatory first line ! #!/usr/local/bin/perl print “Hello everyone\n”; Draw something to the screen

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

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

  11. Perl Calculator $c = 4 - 2; - subtract $c = 2 * 2; - multiply $c = 2 / 2; - divide $c = 2 ** 4; - power : 2^4 <-> 24 =16 $c = 1.35 * 2 – log(3) / (0.12 + 1); natural log

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

  13. Datatypes # - comment line (Perl ignores) Perl Examples: # 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

  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 2. Termination (stop if this is not true) for ( $n=1 ; $n<=100 ; $n+=1 ) { … } 4. Increment ($n = $n + 1) 3. Body (or block) of the loop - commands inside curly brackets

  15. FOR Loop Example Source code: 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”; } Indent =  TA Output - Triangle of A’s: AAAAAA

  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 With numbers: With strings: $x = 1; $y = 2; if ($x < $y) { } if ($x > $y) { } if ($x <= $y) { } if ($x >= $y) { } if ($x == $y) { } if ($x != $y) { } $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) { } Less than Greater than Less than or equal Greater than or equal Equal Not equal

  18. Conditional Statements Source code: $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”; } Output: x = -1 is negative

  19. Conditional Statements The same thing: $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”; } if ( some_expression ) { … } else { … } if this is true do this otherwise do 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); @ - indicates an array (…) - a list of values $a[2] - an element of the array (count from 0) # array of strings @day = (“Mon”, “Tue”, “Wed”, “Thu”, “Fri”);

  22. Data Structures : Arrays @a = (7,3,4,-1); # change the value of an element $a[1] = 5; $#a - the index of the last element in the array @a # print all the elements in the array @a for ($i=0; $i<=$#a; $i+=1) { print “a[$i] = $a[$i] \n”; } 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 ReadorWrite (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 READINGopen (FILE, "<data.txt" ); Directionof file data flow File handler -This name will be used everywhere later in the program, when we will deal with this file. < - READ from a file > - WRITE to a file # close a file specified by FILE file handlerclose (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 readingopen (FILE, “<data.txt”); # read file line by line and print it out to the screen while ($line = <FILE>) { print “$line”; } #close file close(FILE); Read the next line from the file specified by the filehandle <FILE> whileloop is analogous to the forloop. All the body statements of it are executed until the condition in parenthesis is false.

  28. Working with Files 1 18 23 2 Example. Calculating a sum of numbers in the file data.txt: #!/usr/local/bin/perl $sum = 0; open (FILE, “<data.txt”); while ($line = <FILE>) { 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

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

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

  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

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