1. Computer Programming for Biologists Class 3 Nov 13 th, 2014 Karsten Hokamp http://bioinf.gen.tcd.ie/GE3M25

2.  quiz, recap  operator short-cuts  arrays  control structures  comparisons  project Overview Computer Programming for Biologists

3. Scalar variables:  $name = value;  right-to-left assignment  value: numbers or strings of characters  default variable $_  special character: \n (newline)  Evaluation within double quotes e.g.: $text = "$input\n"; $text = '$input\n';  no evaluation Recap Computer Programming for Biologists

4. Variable name delimiter:  $text; # same as  ${text};  useful if text follows variable name, e.g.: $item = 'apple'; print "I bought 4 $items"; # wrong print "I bought 4 ${item}s"; # correct print "I bought 4 ". $item. "s"; # correct Addition to scalars

5. functions for scalars:. (concatenation).= (extension) lc, uc, lcfirst, ucfirst (capitalisation) chop, chomp (removing characters) length reverse substr (extracting parts of a string) tr (transliteration) Recap Computer Programming for Biologists

6.  increase value by one: $counter = $counter + 1; same as $counter++; same as $counter += 1; Operator shortcuts  other shortcuts: $num += 10; $num -= 5; $num1 *= $num2; $num1 /= $num2; $num1 **= 3 $first_name.= $last;  operator combined with '=' applies operation to variable on the left Shortcuts

7. Computer Programming for Biologists Practical session:  Go to http://bioinf.gen.tcd.ie/GE3M25/class3 and try the 'Operators' exercises Operators

8. Computer Programming for Biologists Variables

9. Computer Programming for Biologists Array examples:  @letters = ('a', 'b', 'c', 'd', 'e', 'f');  @numbers = (1, 2, 3, 4, 5, 6, 7, 8, 9, 10);  @names = ('Karsten', 'Devin', 'Ken');  @dates = ('19/01/2007', '26/01/2007');  @block = ($start, $middle, $end); Variables ordered list array variable

10. Computer Programming for Biologists @letters = ('a', 'b', 'c', 'd', 'e', 'f'); @letters = (a..f); # same @numbers = (1..10); # only works ascending  use variables as range limits: $start = 1; $end = 10; @numbers = ($start.. $end);  combine arrays: @hex = (@numbers, @letters); # (1..10, a..f) Array Construction range operator

11. Computer Programming for Biologists  Each element is an individual scalar identified by its index $numbers[0];  Use an expression as index: $i = 0; print $numbers[$i]; # prints first element print $numbers[$i + 1]; # prints second element Array Access array nameindex Note: @ changes to $

12. Special indices and length  length of an array: @numbers = (1..10); $length = scalar @numbers;  last index: $#numbers (one less than length) $numbers[$#numbers]  refers to last element  negative index: $numbers[-1]  refers to last element $numbers[-2]  refers to second last element t Computer Programming for Biologists

13. Scalar and List Context @bases = ('a', 'c', 'g', 't'); # list @bases2 = reverse @bases; # list $bases = @bases; # scalar print @bases; # list print scalar @bases; # scalar print ''.@bases.''; # scalar Computer Programming for Biologists The context determines how a list is treated:

14. Computer Programming for Biologists Practical session:  Go to http://bioinf.gen.tcd.ie/GE3M25/class3 and try the 'Arrays' exercises Arrays

15. Basic Built-in functions for arrays  Adding and removing elements: push, pop (apply to end of array): push @numbers, 11; $last = pop @numbers; shift, unshift (apply to start of array): unshift @numbers, 0; $first = shift @numbers; Computer Programming for Biologists

16. @array, add-on 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 removed = @array Basic Built-in functions for arrays Computer Programming for Biologists shift unshiftpush pop Special variable @ARGV  command line arguments $next_arg = shift @ARGV $next_arg = shift;

17. More Built-in functions for arrays  You will practise these in class! join (joins a list into a string) scalar (returns the length of an array) sort (sorts a list) reverse (reverses a list) splice (removing or adding slices) example: $sequence = join '-', (a..f);  $sequence: 'a-b-c-d-e-f' Computer Programming for Biologists

18. Practical session:  Go to http://bioinf.gen.tcd.ie/GE3M25/class3 and try the 'Arrays' exercises Arrays

19. Control Structures Computer Programming for Biologists

20. Loops  cycle through elements of a list  apply same processing steps each time Computer Programming for Biologists foreach $letter (a..z) { print "$letter\n"; } foreach element (list) { statements } (a..z)  list of characters $letter  single element foreach  type of loop ()  contains list {}  contains statement(s)

21. Loops  cycle while an expression returns something true or content Computer Programming for Biologists while (@array) { $last = pop @array; } Cycle through all elements of an array until (length($seq) < 3) { $cod = substr $seq, 0, 3, ''; } Cycle through all codons of a sequence while ($in = <>) { $input.= $in; } Go through all lines from standard input

22. if ($num > 100) { die "$num is too high!"; } elsif ($num < 1) { die "$num is too low!"; } Branching  if / else / elsif structure Pseudo code: Computer Programming for Biologists Perl code: if (expression) { statements; } else { statements; } if number is too big stop with error message else if number is too small stop with error message if a condition is true then do one thing else do another thing

23. Branching  if / else / elsif structure test for multiple conditions: Computer Programming for Biologists if ($response eq 'y') { print "ok!\n"; } elsif ($response eq 'n') { print "maybe next time\n"; } elsif ($response eq '') { print "please try again: "; } else { print "don't know what you mean\n"; }

24. Comparisons  compare one scalar (or expression) to another numericalalphabetical >, >=gt <, <=lt ==eq !=ne Computer Programming for Biologists  common mistake: $num = 10 is NOT a comparison!

25. True and False  false  0 or empty string ('')  true  value different from 0 (1 by default) Computer Programming for Biologists ComparisonEvaluationBoolean 5 > 2 2 > 5 a > b 'ACTG' eq 'actg' '1' ne '1.0' 2+2 == 8/2  Comparisons are last in order of execution!

26. True and False  false  0 or empty string ('')  true  value different from 0 (1 by default) Computer Programming for Biologists ComparisonEvaluationBoolean 5 > 21TRUE 2 > 50FALSE a > b0FALSE 'ACTG' eq 'actg'0FALSE '1' ne '1.0'1TRUE 2+2 == 8/21TRUE  Comparisons are last in order of execution!

27. Computer Programming for Biologists Practical session:  Go to http://bioinf.gen.tcd.ie/GE3M25/class3 and try the 'Controls' exercises Control Structures

28. Computer Programming for Biologists Implement the following in a program: 1. Print a welcome message 2. Read input from a file 3. Separate header from sequence 4. Report length of sequence 5. Make sequence all upper case 6. Reformat sequence into 60 bp width 7. Print reverse-complement 8. Provide position numbers at each line  Go to http://bioinf.gen.tcd.ie/GE3M25/class3 Project