1. Books

2. Perl Perl (Practical Extraction and Report Language) by Larry Wall Perl 1.0 was released to usenet's alt.comp.sources in 1987 Perl 5 was released in 1994. Low Level lang. (C/C++,Pascal) – hard to write, fast runtime, unlimited. High Level lang. (shell, awk, …) – hard, slow, very limited. Perl – easy, mostly fast, nearly unlimited.

3. Perl Optimized to work with text Free source code, very good support www.cpan.orgwww.cpan.org (Perl source, docs, extensions) www.perldoc.com/ Perl for Windows www.activestate.comwww.activestate.com

4. Just for Start Returns a list of strings from the input files Sorts the list Prints the list >sort.pl *.txt #!/usr/bin/perl print sort ; sort.pl

5. Hello Perl On Unix create text file, “hello.pl” (any name/extension is ok): #!/usr/bin/perl print “Hello, Perl!\n”; #comment your code $var1= “Hello, World!”. ”\n”; #No variable declaration is needed print $var1; $ivar += 10; #scalar variables initialized with 0 # (strings with empty string “” ) print “This is $ivar \n”;

6. Hello Perl (2) Set on executable flag: >chmod +x hello.pl Run it: >hello.pl #!/usr/bin/perl always use this header (without any spaces)

7. Strings ‘Hello Perl\n’ not equal to “Hello Perl\n” ‘Hello $var’ not equal to “Hello $var” Concatenation : “Hello”. ”Perl\n” = “Hello Perl\n” Copy: “Perl” x 3 = “PerlPerlPerl”

8. Print print “hello ”; print 3*$ivar; print “\n”; print “hello “, 3*$ivar, “\n”; $world=“world”; print “hello “, $world, “\n”; print “hello “. $world. “\n”; print “hello $world \n”; print “hello ${world}s \n”;

9. Comparison Operators ComparisonNumericString Equal==eq Not equal!=ne Less than<lt Greater than>gt Less than or equal to<=le Greater than or equal to>=ge If( $ivar != 5) … If( $str ne “hello”) …

10. Binary Operators a + b a – b a * b a / b a ** b a b a % bmodulus Unary Operators Changing Sign +a positive operand -a negative operand Changing Value Before Usage ++a $a=3; $b= ++$a; #b=4, a=4 --a Changing Value After Usage a++ $a=3; $b= $a++; #b=3, a=4 a--

11. User Input $line= ; while ($line= ){ chomp($line); #remove new line char \n if($line eq “quit”){ exit(0); }

12. Arrays $rocks[0]=“bedrock”; $rocks[1]=“lava”; $rocks[99]=“rock”; # now there are 100 elements print “$rocks[ $#rocks ] \n”; # prints last element ‘rock’ $size = $#rocks + 1; #number of elements

13. Lists (0,5,6,7,8); (0,5..8); # (..) range operator (0,”5..8”); # contains two elements 0 and string “5…8”

14. List Assignment ($color, $tree, $list) = (“green”, “red-black”, “linked”); #swap ($color, $tree) = ($tree, $color); ($i, $j)=(1..3); # 3 – is ignored ($i, $j, $k)=(1,2); # $k gets undef

15. List Assignment (2) ($color[0], $color[1], $color[2])=(“red”, “blue”, “green”); @colors=(“red”, “blue”, “green”); @more_colors=(“white”, @colors, “yellow”); # more_colors contains “white”, “red”, “blue”, “green”, “yellow” print “Five colors: @more_colors. \n”; #five colors: white red blue green yellow.

16. Foreach @colors=(“red”, “blue”, “green”); for($i=0;$i <= $#colors; $i++){ print “$colors[$i] \n”; } #other way to do the same #but array is changed foreach $col (@colors){ $col.= “\n”; } print @colors; #much better foreach $col (@colors){ print “$col \n”; }

17. Push and Pop @array= 1..5; push @array, 6; #array contains 1..6 $six= pop @array; #array contains 1..5 @others= 6..10; push @array, @others; #array contains 1..10

18. Shift and Unshift Push and Pop – for the end of an array Shift and Unshift – for the start of an array @array= 1..5; $five = shift @array; #array contains 2…5 unshift @array, 1; #array contains 1…5 unshift @array, (-2,-1,0); #array contains –2…5 ! Shift and Unshift, unlike Push and Pop, change indices of all array elements

19. Default variable $_ @colors=(“red”, “blue”, “green”); foreach (@colors){ $_.= “ \n”; } $_ = “default variable\n”; print; #prints “default variable\n”

20. Reverse, Sort operators @array= 1..100; print reverse(@array); @array= reverse (@array); #array contains 100..1 #sorts in ASCII order @array= sort (@array); #array contains 1, 100,11,12 … 19,2,20,…,9,90…99

21. in List Context open FILE, “readme.txt” or die “Cannot open file: $!”; while ($line= ){ chomp($line); #remove new line char \n push @lines, $line; } # or this way chomp ( @lines = ); #better way @lines = ; chomp( @lines );

22. Perl is Context Dependent @sorted_array= sort @array; #list context $ii = 3 + @array; #scalar context: 3+ArraySize ($ii) = @array; #list context: $ii=$array[0] @array = 38; #list context: @array=(38) $str= ; #return next line form FILE @lines= ; #returns all remaining lines

23. Example Task: Write a program that prints each line in a right- justified 20 character column. First print a “ruler-line” of digits. 1234567890 123456789012345678901234567890 hello test-test 20

24. Example (solution) chomp( @lines= ); print “1234567890” x 7, “\n”; foreach (@lines){ printf “%20s\n”, $_; } $format = “%20s\n” x @lines; printf $format, @lines; For more info on printf run: perldoc –f sprintf

25. Control Statements: unless, until if( $a != $b){ } unless ( $a== $b){ } while( $a > $b){ } until( $a<=$b ){ }

26. Control Statements: elsif if ( expression1 ){ }elsif(expression2 ){ }elsif(expression3 ){ }else{ } Only the block of the first true conditional expression is executed, or else otherwise.

27. Control Statements: next, last while( ){ if( /Protein ID/ ){ print ; next; } ……….. if( /Remarks/ ){ last; }

28. Control Statements: redo while ( … ) { if( … ){ redo; #starts the current iteration from the beginning (control # statement is not evaluated) #notice the difference with the next (starts the next iteration) }

29. Control Statements: logical operator $proteinID = $proteins{ $id } or “Unknown”; #or like in C - expression ? TrueExpression : FalseExpression; $proteinID = $proteins{ $id } ? $proteins{ $id } : “Unknown”;

30. Example: Parsing FASTA file >roa1_drome Rea guano receptor type III >> 0.1 MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV VMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK KLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQK QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY >roa2_drome Rea guano ligand MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV VMKDPTSTSTSTSTSTSTSTSTMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK KLFVGALKDDHDEQSIRDYFQHLLLLLLLDLLLLDLLLLDLLLFVEFDDYDPVDKVVLQK QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY

31. Example: Parsing FASTA file (2) print “Input file name:”; $filename= ; open FASTA, $filename; @lines= ; foreach $line (@lines){ f($line =~ /^\s*$/){ next; #continue if empty line } if($line =~ />/){ print "Header:", $line; }else{ print "Seq:", $line; } Parses file in FASTA format. Filename is input to the program.

32. Example: Parsing FASTA file (3) die "Can't open file:$ARGV[0]" unless open( FASTA, $ARGV[0]); @lines= ; foreach (@lines){ unless( /^\s*$/ ){ #continue if empty line if( />/ ){ print "Header:", $_; }else{ print "Seq:", $_; } Parses file in FASTA format. Filename is argument to the program.

33. Example: Parsing FASTA file (4) @lines= <>; foreach (@lines){ unless( /^\s*$/ ){ #continue if empty line if( />/ ){ print "Header:", $_; }else{ print "Seq:", $_; } Parses file in FASTA format. Filenames are arguments to the program. Automatic error message in case of invalid filename. Reads all input files (from the argument list)

34. Example: Parsing FASTA file (5) while ( <> ){ unless( /^\s*$/ ){ #continue if empty line if( />/ ){ print "Header:", $_; }else{ print "Seq:", $_; } Parses file in FASTA format. Filenames are arguments to the program.

35. HomeWork (a)Parsing FASTA file. Write two separate programs. Read FASTA file. Output reverse sequence in FASTA format. Hint: use split function (perldoc –f split). For DNA sequence output reverse complement. Hint: use substr function (perldoc –f substr) (c) Create your personal I-net Home Page.