Practical Extraction and Report Language. «Perl is a language of getting your job done» «There is more than one way to do it»

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1 Practical Extraction and Report Language «Perl is a language of getting your job done» «There is more than one way to do it» IOANNIDIS Vassilios Swiss Institute of Bioinformatics EMBnet Group Quartier Sorge - Batiment Genopode CH-1015 Lausanne - Switzerland T: vassilios.ioannidis@isb-sib.ch Larry Wall VI, September 2008 Page 1 Perl Outline : Filehandles & File Tests Subroutines (functions) References passing arguments to functions nested data structure Packages/Modules Namespace/@INC VI, September 2008 Page 2

2 Perl Files vioannid$ less list_dos.txt Mrs. Bausch Damaris^MMr. Burckhardt Christoph^MDr. (Mrs.) Casado Begona^MMr. Dalla Torre Simon^MMr. Hammann Felix^MDr. (Mr.) Heller Manfred^MMr. Hurschler Benjamin^MMr. Klemm Sebastian^MMrs. List Claudia^MMr. Ludin Philipp^MMr. Mannhart Lukas^MMrs. Mathimaran Vinodha^MDr. (Mr.) Muller Andreas^MMrs. Oberhansli Simone^MMrs. Roltgen Katharina^MDr. (Mrs.) Schweizer Magali^MMrs. Suenderhauf Claudia^MDr. (Mr.) Tzouros Manuel^MMrs. Uplekar Swapna^MDr. (Mrs.) Vuillet Laurie^MMr. Watkins Stephan Lloyd^MMr. Young Thomas vioannid$ od -c list_dos.txt M r s. \t B a u s c h \t D a m a r i s \r M r. \t B u r c k h a r d t \t C h r i s t o p h \r D r ( M r s. ) \t C a s a d o \t B e g o n a \r M r. \t D a l l a T o r r e \t S i m o n \r M r. \t H a m m a n n \t F e l i x \r D r ( M r. ) \t H e l l e r \t M a n f r e d \r M r. \t H u r s c h l e r \t B e n j a m i n \r M r \t K l e m m \t S e b a s t i a n \r M r s. \t L i s t \t C l a u d i a \r M r. \t L u d i n \t P h i l i p p \r M r. \t M a n n h a r t \t L u k a s \r M r s. \t M a t h i m a r a n \t V i n o d h a \r D r. ( M r. ) \t M u l l e r \t A n d r e a s \r M r s. \t O Important: Unix & all Unix flavors: Mac OS : Windows: \n \r \r\n Unix command: tr vioannid$ tr '\r' '\n' < list_dos.txt > list.txt Perl command: s/// vioannid$ perl -p -e 's/\r/\n/g' < list_dos.txt > list.txt VI, September 2008 Page 3 Perl Files vioannid$ less list.txt Mrs. Bausch Damaris Mr. Burckhardt Christoph Dr. (Mrs.) Casado Begona Mr. Dalla Torre Simon Mr. Hammann Felix Dr. (Mr.) Heller Manfred Mr. Hurschler Benjamin Mr. Klemm Sebastian Mrs. List Claudia Mr. Ludin Philipp Mr. Mannhart Lukas Mrs. Mathimaran Vinodha Dr. (Mr.) Muller Andreas Mrs. Oberhansli Simone Mrs. Roltgen Katharina Dr. (Mrs.) Schweizer Magali Mrs. Suenderhauf Claudia Dr. (Mr.) Tzouros Manuel Mrs. Uplekar Swapna Dr. (Mrs.) Vuillet Laurie Mr. Watkins Stephan Lloyd Mr. Young Thomas VI, September 2008 vioannid$ od -c list_dos.txt M r s. \t B a u s c h \t D a m a r i s \n M r. \t B u r c k h a r d t \t C h r i s t o p h \n D r ( M r s. ) \t C a s a d o \t B e g o n a \n M r. \t D a l l a T o r r e \t S i m o n \n M r. \t H a m m a n n \t F e l i x \n D r ( M r. ) \t H e l l e r \t M a n f r e d \n M r. \t H u r s c h l e r \t B e n j a m i n \n M r \t K l e m m \t S e b a s t i a n \n M r s. \t L i s t \t C l a u d i a \n M r. \t L u d i n \t P h i l i p p \n M r. \t M a n n h a r t \t L u k a s \n M r s. \t M a t h i m a r a n \t V i n o d h a \n D r. ( M r. ) \t M u l l e r \t A n d r e a s \n M r s. \t O b e r h a n s l i \t S i m o n e Page 4

3 Perl Filehandles A filehandle is the name in a Perl program for an I/O connection between your Perl process and the outside world. (Good practice: use all uppercase letters in the name of your filehandle) Perl special file handles There are three connections that always exist and are always "open" when your program starts: STDIN, STDOUT, and STDERR. Actually, these names are file handles. File handles are variables used to manipulate files. STDIN reads from standard input which is usually the keyboard in normal Perl script (or input from a Browser in a CGI script. Cgi-lib.pl reads from this automatically.) STDOUT (standard output) and STDERR (standard error) by default write to a console (or a browser in CGI). We have been using the STDOUT file handle without knowing it for every print() statement during Perl presentations. The print() function uses STDOUT as the default if no other file handle is specified. VI, September 2008 Page 5 Perl - Getting User Input How to get a value from the keyboard into a Perl program? The simplest way is to use the line-input operator: <STDIN> Each time we use <STDIN> in a place where a scalar value is expected, Perl reads the next complete text line up to the first newline from the keyboard (unless you modified it). print "Please enter your Lastname: "; my $lastname = <STDIN>; chomp $lastname; Please enter your Lastname: Ioannidis print "Please enter your Firstname: "; my $firstname = <STDIN>; chomp $firstname; Please enter your Firstname: Hello Vassilios Ioannidis, I hope you like Perl programming! Vassilios print "Hello $firstname $lastname,\n I hope you like Perl programming!\n"; exit; VI, September 2008 Page 6

4 Perl Filehandles vioannid$ cat course_list.csv List;Claudia;Mrs.;Basel;4051; Hammann;Felix;Mr.;Basel;4031; Vuillet;Laurie;Dr. (Mrs.) ;Lausanne;1015; Suenderhauf;Claudia;Mrs.;Basel;4058; Roltgen;Katharina;Mrs.;Basel;4051; Klemm;Sebastian;Mr.;Basel;4056; Young;Thomas;Mr.;Zurich;8032; Muller;Andreas;Dr. (Mr.);Basel;4002; Schweizer;Magali;Dr. (Mrs.) ;Zurich;8092; Watkins;Stephan Lloyd;Mr.;Bern;3012; Tzouros;Manuel;Dr. (Mr.);Basel;4070; Uplekar;Swapna;Mrs.;Lausanne;1015; Burckhardt;Christoph;Mr.;Zurich;8057; Mathimaran;Vinodha;Mrs.;Basel;4056; Oberhansli;Simone;Mrs.;Zurich;8008; Ludin;Philipp;Mr.;Bern;3012; Bausch;Damaris;Mrs.;Zurich;8093; Dalla Torre;Simon;Mr.;Basel;4056; Casado;Begona;Dr. (Mrs.) ;Lausanne;1000; Mannhart;Lukas;Mr.;Basel;4058; Hurschler;Benjamin;Mr.;Basel;4058; vioannid VI, September 2008 Page 7 The invocation Perl Filehandles open (FILE, "course_list.csv") or die "Error. Could not open the file!\n"; while (<FILE>) { if (m/^(.*);(.*);(.*);(.*);(.*);$/) { print "Hello $3 $2 $1 from $4!\n"; else { exit; vioannid$./course_list.pl Hello Mrs. Claudia List from Basel! Hello Mr. Felix Hammann from Basel! Hello Dr. (Mrs.) Laurie Vuillet from Lausanne! Hello Mrs. Claudia Suenderhauf from Basel! Hello Mrs. Katharina Roltgen from Basel! Hello Mr. Sebastian Klemm from Basel! Hello Mr. Thomas Young from Zurich! Hello Dr. (Mr.) Andreas Muller from Basel! Hello Dr. (Mrs.) Magali Schweizer from Zurich! Hello Mr. Stephan Lloyd Watkins from Bern! Hello Dr. (Mr.) Manuel Tzouros from Basel! Hello Mrs. Swapna Uplekar from Lausanne! Hello Mr. Christoph Burckhardt from Zurich! Hello Mrs. Vinodha Mathimaran from Basel! Hello Mrs. Simone Oberhansli from Zurich! Hello Mr. Philipp Ludin from Bern! Hello Mrs. Damaris Bausch from Zurich! Hello Mr. Simon Dalla Torre from Basel! Hello Dr. (Mrs.) Begona Casado from Lausanne! Hello Mr. Lukas Mannhart from Basel! Hello Mr. Benjamin Hurschler from Basel! VI, September 2008 Page 8

5 Perl Filehandles The invocation Technically, the diamond <> operator is not looking literally at the invocation argument. It works from array. This is a special array that is preset by Perl to be a list of the invocation arguments. When the program contains the list of invocation arguments. And can be handled as a just like any other array! vioannid$./argv1.pl course_list.csv course_list.csv my $nb_arg my $argument = $ARGV[0]; print "\n$nb_arg\n"; print "The invocation argument is: $argument\n"; 1 The invocation argument is: course_list.csv exit; VI, September 2008 Page 9 The invocation Perl Filehandles my $filename = $ARGV[0]; open (FILE, "$filename") or die "Error. Could not open the file $filename!\n"; while (<FILE>) { if (m/^(.*);(.*);(.*);(.*);(.*);$/) { print "Hello $3 $2 $1 from $4!\n"; else { exit; vioannid$./argv2.pl course_list.csv Hello Mrs. Claudia List from Basel! Hello Mr. Felix Hammann from Basel! Hello Dr. (Mrs.) Laurie Vuillet from Lausanne! Hello Mrs. Claudia Suenderhauf from Basel! Hello Mrs. Katharina Roltgen from Basel! Hello Mr. Sebastian Klemm from Basel! Hello Mr. Thomas Young from Zurich! Hello Dr. (Mr.) Andreas Muller from Basel! Hello Dr. (Mrs.) Magali Schweizer from Zurich! Hello Mr. Stephan Lloyd Watkins from Bern! Hello Dr. (Mr.) Manuel Tzouros from Basel! Hello Mrs. Swapna Uplekar from Lausanne! Hello Mr. Christoph Burckhardt from Zurich! Hello Mrs. Vinodha Mathimaran from Basel! Hello Mrs. Simone Oberhansli from Zurich! Hello Mr. Philipp Ludin from Bern! Hello Mrs. Damaris Bausch from Zurich! Hello Mr. Simon Dalla Torre from Basel! Hello Dr. (Mrs.) Begona Casado from Lausanne! Hello Mr. Lukas Mannhart from Basel! Hello Mr. Benjamin Hurschler from Basel! VI, September 2008 Page 10

6 Perl Filehandles You can open a file for input or output using the open() function. open(infile, "input.txt") or die "Can't open input.txt: $!"; open(outfile, ">output.txt") or die "Can't open output.txt: $!"; open(logfile, ">>logfile") or die "Can't open logfile: $!"; You can use your own naming instead of "INFILE", "OUTFILE" or "LOGFILE". When you're done with your filehandles, you should close() them (though Perl will clean up after you if you forget ): close INFILE; print() can also take an optional first argument specifying which filehandle to print to: print STDERR "This is your final warning\n"; print OUTFILE $record; print LOGFILE $logmessage; use whatever name you like BUT: STDIN, STDOUT, STDERR, ARGV! VI, September 2008 Page 11 Perl Filehandles File test Meaning -r File is readable by effective user/group. -w File is writable by effective user/group. -x File is executable by effective user/group. -o File is owned by effective user. -R File is readable by real user/group. -W File is writable by real user/group. -X File is executable by real user/group. -O File is owned by real user. -e File exists. -z File has zero size. -s File has nonzero size (returns size). -f File is a plain file. -d File is a directory. -l File is a symbolic link. File test Meaning -p File is a named pipe (FIFO). -S File is a socket. -b File is a block special file. -c File is a character special file. -t Filehandle is opened to a tty. -u File has setuser bit set. -g File has setgroup bit set. -k File has sticky bit set. -T File is a text file. -B File is a binary file (opposite of -T). -M Age of file (at startup) in days since modification. -A Age of file (at startup) in days since last access. -C Age of file (at startup) in days since inode change. VI, September 2008 Page if (-e $filename) { #do something...

7 Perl Filehandles You can read from an open filehandle using the "<>" operator. In scalar context it reads a single line (or a single record) from the filehandle, and in list context it reads the whole file in, assigning each line to an element of the list: my $line = <INFILE>; = <INFILE>; Reading in the whole file at one time is called slurping. It can be useful but it may be a memory hog. Most text file processing can be done a line at a time with Perl's looping constructs. The "<>" operator is most often seen in a while loop: while (<INFILE>) { # assigns each line in turn to $_ print "Just read in this line: $_"; close INFILE; VI, September 2008 Page 13 Perl Filehandles You can read from an open filehandle using the "<>" operator. In scalar context it reads a single line (or a single record) from the filehandle. Most text file processing can be done a line at a time with Perl's looping constructs. The "<>" operator is most often seen in a while loop: >3BHS1_RAT PGWSCLVTGAGGFVGQRIIRMLVQEKELQEVRALDKVFRPETKEEFSKLQTKAKVTMLEG DILDAQYLRRACQGISVVIHTAAVIDVSHVLPRQTILDVNLKGTQNILEACVEASVPAFI YCSTVDVAGPNSYKKIILNGHEEEHHESTWSDAYPYSKRMAEKAVLAANGSILKNGGTLH TCALRPMYIYGERSPFLSVMILAALKNKGILNVTGKFSIANPVYVGNVAWAHILAARGLR DPKKSQNVQGQFYYISDDTPHQSYDDLNCTLSKEWGLRLDSSWSLPLPLLYWLAFLLETV SFLLRPFYNYRPPFNCHLVTLSNSKFTFSYKKAQRDLGYVPLVSWEEAKQKTSEWIGTLV EQHRETLDTKSQ >3BHS2_RAT PGWSCLVTGAGGFVGQRIIRMLVQEKELQEVRALDKVFRPETKEEFSKLQTKAKVTMLEG DILDAQYLRRACQGISVVIHTASVMDFSRVLPRQTILDVNLKGTQNLLEAGIHASVPAFI YCSTVDVAGPNSYKKTILNGREEEHHESTWSNPYPYSKKMAEKAVLAANGSILKNGGTLH TCALRPMYIYGERGQFLSRIIIMALKNKGVLNVTGKFSIVNPVYVGNVAWAHILAARGLR DPKKSQNIQGQFYYISDDTPHQSYDDLNCTLSKEWGLRLDSSWSLPLPLLYWLAFLLETV SFLLRPFYNYRPPFNCHLVTLSNSKFTFSYKKAQRDLGYEPLVSWEEAKQKTSEWIGTLV EQHRETLDTKSQ >3BHS4_RAT PGWSCLVTGAGGFLGQRIVQLLVQEKDLKEVRVLDKVFRPETREEFFNLGTSIKVTVLEG DILDTQCLRRACQGISVVIHTAALIDVTGVNPRQTILDVNLKGTQNLLEACVQASVPAFI... VI, September 2008 Page 14

8 Perl Filehandles You can read from an open filehandle using the "<>" operator. In scalar context it reads a single line (or a single record) from the filehandle. Most text file processing can be done a line at a time with Perl's looping constructs. The "<>" operator is most often seen in a while loop: ID 3BHS1_RAT STANDARD; PRT; 372 AA. AC P22071;..... SQ SEQUENCE 372 AA; MW; F989617C1AF18949 CRC64; PGWSCLVTGA GGFVGQRIIR MLVQEKELQE VRALDKVFRP ETKEEFSKLQ TKAKVTMLEG DILDAQYLRR ACQGISVVIH TAAVIDVSHV LPRQTILDVN LKGTQNILEA CVEASVPAFI YCSTVDVAGP NSYKKIILNG HEEEHHESTW SDAYPYSKRM AEKAVLAANG SILKNGGTLH TCALRPMYIY GERSPFLSVM ILAALKNKGI LNVTGKFSIA NPVYVGNVAW AHILAARGLR DPKKSQNVQG QFYYISDDTP HQSYDDLNCT LSKEWGLRLD SSWSLPLPLL YWLAFLLETV SFLLRPFYNY RPPFNCHLVT LSNSKFTFSY KKAQRDLGYV PLVSWEEAKQ KTSEWIGTLV EQHRETLDTK SQ // ID 3BHS2_RAT STANDARD; PRT; 372 AA. AC P22072;..... SQ SEQUENCE 372 AA; MW; EDAB175F3F33334B CRC64; PGWSCLVTGA GGFVGQRIIR MLVQEKELQE VRALDKVFRP ETKEEFSKLQ TKAKVTMLEG DILDAQYLRR ACQGISVVIH TASVMDFSRV LPRQTILDVN LKGTQNLLEA GIHASVPAFI YCSTVDVAGP NSYKKTILNG REEEHHESTW SNPYPYSKKM AEKAVLAANG SILKNGGTLH TCALRPMYIY GERGQFLSRI IIMALKNKGV LNVTGKFSIV NPVYVGNVAW AHILAARGLR DPKKSQNIQG QFYYISDDTP HQSYDDLNCT LSKEWGLRLD SSWSLPLPLL YWLAFLLETV SFLLRPFYNY RPPFNCHLVT LSNSKFTFSY KKAQRDLGYE PLVSWEEAKQ KTSEWIGTLV EQHRETLDTK SQ // VI, September 2008 Page 15 Perl Filehandles You can modify the regular record separator "\n" by something else: $/= "\n//\n"; for a file containing SwissProt entries or $/=">"; for a fasta file $/=">"; while (<INFILE>) { # assigns each line in turn to $_ print "Entry: $_"; vioannid$./any_script.pl Entry:>Entry:3BHS1_RAT PGWSCLVTGAGGFVGQRIIRMLVQEKELQEVRALDKVFRPETKEEFSKLQTKAKVTMLEG DILDAQYLRRACQGISVVIHTAAVIDVSHVLPRQTILDVNLKGTQNILEACVEASVPAFI YCSTVDVAGPNSYKKIILNGHEEEHHESTWSDAYPYSKRMAEKAVLAANGSILKNGGTLH TCALRPMYIYGERSPFLSVMILAALKNKGILNVTGKFSIANPVYVGNVAWAHILAARGLR DPKKSQNVQGQFYYISDDTPHQSYDDLNCTLSKEWGLRLDSSWSLPLPLLYWLAFLLETV SFLLRPFYNYRPPFNCHLVTLSNSKFTFSYKKAQRDLGYVPLVSWEEAKQKTSEWIGTLV EQHRETLDTKSQ >Entry:3BHS2_RAT PGWSCLVTGAGGFVGQRIIRMLVQEKELQEVRALDKVFRPETKEEFSKLQTKAKVTMLEG DILDAQYLRRACQGISVVIHTASVMDFSRVLPRQTILDVNLKGTQNLLEAGIHASVPAFI YCSTVDVAGPNSYKKTILNGREEEHHESTWSNPYPYSKKMAEKAVLAANGSILKNGGTLH TCALRPMYIYGERGQFLSRIIIMALKNKGVLNVTGKFSIVNPVYVGNVAWAHILAARGLR DPKKSQNIQGQFYYISDDTPHQSYDDLNCTLSKEWGLRLDSSWSLPLPLLYWLAFLLETV SFLLRPFYNYRPPFNCHLVTLSNSKFTFSYKKAQRDLGYEPLVSWEEAKQKTSEWIGTLV EQHRETLDTKSQ..... VI, September 2008 Page 16

9 Perl Outline : Filehandles & File Tests Subroutines (functions) References passing arguments to functions nested data structure Packages/Modules Namespace/@INC VI, September 2008 Page 17 Perl Subroutines = ("Claudia", "Felix", "Laurie", "Thomas","Simone"); foreach (@names1 ) { my $size = length($_); print '*'x($size+2),"\n"; print "*$_*\n"; print '*'x($size+2),"\n"; exit ; vioannid$./sub1.pl * *Claudia* * ******* *Felix* ******* *Laurie* *Thomas* *Simone* VI, September 2008 Page 18

10 Perl Subroutines = ("Claudia", "Felix", "Laurie", "Thomas","Simone"); foreach (@names1 ) { my $size = length($_); print '*'x($size+2),"\n"; print "*$_*\n"; print '*'x($size+2),"\n"; = ("Benjamin","Lukas","Begona","Simon"); foreach (@names2 ) { my $size = length($_); print '*'x($size+2),"\n"; print "*$_*\n"; print '*'x($size+2),"\n"; = ("Christoph","Swapna","Manuel","Magali"); foreach (@names3 ) { my $size = length($_); print '*'x($size+2),"\n"; print "*$_*\n"; print '*'x($size+2),"\n"; vioannid$./sub2.pl * *Claudia* * ******* *Felix* ******* *Laurie* *Swapna* *Manuel* *Magali* exit ; VI, September 2008 Page 19 Perl Subroutines Functions in Perl are called subroutines A subroutine is a named, reusable, and accessible chunk of code that was written to accomplish a specific goal. Therefore, functions are useful to avoid typing redundant code over and over. Functions help in the clarity of scripts. Don't reinvent the wheel!!! There are already many available functions in Perl: VI, September 2008 Page 20

11 Perl Subroutines (procedure, function) #defining subroutine sub myfunc { my $param = shift(@_);... return $result; # calling a function $calcul = myfunc($value); #defining subroutine sub myproc { my $param = shift(@_);... return; # calling procedure myproc($value); Some Perl commands tell the Perl interpreter to do something. A statement starting with a "verb" is generally purely imperative. We often call these "verbs" procedures: a frequently seen command is the print command. Some verbs are for asking questions, and are useful in conditional statements. Other verbs translate their input parameters into return values, just as a recipe tells you how to turn raw ingredients into something (hopefully) edible. We tend to call these verbs functions. VI, September 2008 Page 21 Perl Subroutines = ("Claudia", "Felix", "Laurie", "Thomas","Simone"); = ("Benjamin","Lukas","Begona","Simon"); = ("Christoph","Swapna","Manuel","Magali"); &pretty_print(@names1); &pretty_print(@names2); &pretty_print(@names3); exit ; sub pretty_print { foreach (@_) { my $size = length($_); print '*'x($size+2),"\n"; print "*$_*\n"; print '*'x($size+2),"\n"; vioannid$./sub3.pl * *Claudia* * ******* *Felix* ******* *Laurie* *Swapna* *Manuel* *Magali* VI, September 2008 Page 22

12 Perl functions #call the helloworld function #& is optional with parentheses helloworld(); vioannid$./sub_hello.pl hello World! vioannid$ #tell the program to exit exit; sub helloworld{ print "hello World!\n"; In the same manner than $ stands for for arrays and % for hashes, & stands for subroutines (optional when () are used). Note, however, that in practice, helloworld(); is preferred to &helloworld; VI, September 2008 Page 23 Perl functions vioannid$./sub_sum.pl 46 vioannid$ # pass 2 arguments to the plus function # receive the output in $sum my $sum = plus(12,34); print "$sum\n"; exit; sub plus{ my($x, $y)=@_; return $x+$y; In order to accomplish this goal a subroutine can sometimes need input, or what are called input parameters. In this case, the list of those parameters will be caught through the default VI, September 2008 Page 24

13 Perl functions vioannid$./sub_sum_array.pl sum=18 vioannid$ 4, 5, 8); my $sum = &plus(@vals); print "sum=$sum\n"; sub plus{ my $add = 0; foreach(@values){ $add += $_; return $add; VI, September 2008 Page 25 Perl functions Checking/Detecting parameters Checking the number of parameters A common problem is to check the number of parameters (and maybe return an is a normal array, therefore: my $nbparam = Detecting a parameter type with ref($x) (is it a scalar? an array reference? a file handle?) ref($x) will return a string with the type of the argument: empty string for scalar, ARRAY for array, HASH for hash table, GLOB for a file handle etc. Detecting the parameters type allows to handle in the same subroutine many different situations. VI, September 2008 Page 26

14 Perl Scope of Variables Scope refers to the visibility of variables. In other words, which parts of your program can see or use them. = ( "Simon","Magali", "Lukas","Swapna" ); vioannid$./scope.pl Global symbol "$name" requires explicit package name at./scope.pl line 12. Execution of./scope.pl aborted due to compilation errors. vioannid$ foreach my $name (@list) { print "Hello $name!\n"; Lexical Scope print "Hello $name!\n"; Lexical scope is more ideal for the majority of variables programmers use regularly. Lexical scope allows a variable exit ; to exist only within its containing closure. The widest scope available to a lexical variable is the entire file in which its declared. No entry is created in the symbol table for lexically scoped variables and these variables will be purged once they're out of scope. This use of Perl's garbage collection can save resources and prevent variable collisions. Lexical scope has to be declared by using Perl's my() function. Variables have to be declared with "use strict". VI, September 2008 Page 27 Perl Scope of Variables my $a = 5; my $b = 10; print '$a before: '."$a\n"; print '$b before: '."$b\n\n"; vioannid$./scope2.pl $a before: 5 $b before: 10 double, $a: 10 double, $b: 20 $a after: 10 $b after: 20 vioannid$ double($a,$b); print '$a after: '."$a\n"; print '$b after: '."$b\n"; exit ; sub double { $a = shift; #$a = $_[0]; $b = shift; #$b = $_[1]; $a=$a*2; $b=$b*2; print 'double, $a: '."$a\n"; print 'double, $b: '."$b\n\n"; VI, September 2008 Page 28

15 Perl Scope of Variables my $a = 5; my $b = 10; print '$a before: '."$a\n"; print '$b before: '."$b\n\n"; vioannid$./scope3.pl $a before: 5 $b before: 10 double, $a: 10 double, $b: 20 $a after: 5 $b after: 10 vioannid$ double($a,$b); print '$a after: '."$a\n"; print '$b after: '."$b\n"; exit ; sub double { my $a = shift; #my $a = $_[0]; my $b = shift; #my $b = $_[1]; $a=$a*2; $b=$b*2; print 'double, $a: '."$a\n"; print 'double, $b: '."$b\n\n"; VI, September 2008 Page 29 Perl functions = ("Claudia", "Felix", "Laurie"); = ("Thomas","Simone"); print "@list1\n"; print "@list2\n"; list(@list1,@list2); exit ; sub list { ; print("the first array print("the second array vioannid$./scope4.pl Claudia Felix Laurie Thomas Simone The first array is Claudia Felix Laurie Thomas Simone. The second array is. VI, September 2008 Page 30

16 Perl Outline : Filehandles & File Tests Subroutines (functions) References passing arguments to functions nested data structure Packages/Modules Namespace/@INC VI, September 2008 Page 31 Perl References References If you want to pass more than one array or hash into a function (or return them from it) and maintain their integrity, then you have to use an explicit pass-byreference In Perl, you can pass only one kind of argument to a subroutine: a scalar. You do that by passing a reference to it. A reference to anything is a scalar. Think at a reference as the Macintosh's alias or the Windows's shortcut. VI, September 2008 Page 32

17 Perl References References If you want to pass more than one array or hash into a function (or return them from it) and maintain their integrity, then you have to use an explicit pass-byreference In Perl, you can pass only one kind of argument to a subroutine: a scalar. You do that by passing a reference to it. A reference to anything is a scalar. Think at a reference as the Macintosh's alias or the Windows's shortcut. (an array with \@list_names value john magdalena luc john magdalena luc 0x180b324 "address" 0x180b524 0x180b324 0x180b318 VI, September 2008 Page 33 Perl References = ("Laurie", "Felix", "Claudia"); = ("Thomas","Simone"); print "\nbefore the list function:\n"; print "list print "list list(\@list1,\@list2); print "\n\nafter the list function:\n"; print "@list1\n"; print "@list2\n\n"; exit ; vioannid$./scope5.pl Before the list function: list 1: Laurie Felix Claudia list 2: Thomas Simone Within the list function: list 1: Claudia Felix Laurie. list 2: Simone Thomas. After the list function: Claudia Felix Laurie Simone Thomas sub list { my $ref1 = shift; my $ref2 = = print "\n\nwithin the list function:\n"; print "list print "list VI, September 2008 Page 34

18 Perl References References The following table discusses the referencing and de-referencing of variables. Note that in the case of lists and hashes, you reference and dereference the list or hash as a whole, not individual elements. Variable Instantiating the scalar Instantiating a reference to it Referencing it Dereferencing it Accessing an element $scalar $scalar="steve"; ${$ref $ref = \$scalar $$ref = ( "steve", "fred" ); $ref = [ "steve", "fred" ]; $ref ${$ref[1] $ref->[1] %hash %hash = ( "name" => "steve", "job" => "DJ" ); $hash = { "name" => "steve", "job" => "DJ" ; $ref = \%hash %{$ref %$ref ${$ref{"name" $ref->{"job" VI, September 2008 Page 35 Perl References References vioannid$./ref1.pl my %hash = ( "name" => "steve", "job" => "DJ" ); my $ref = \%hash; print ${$ref{"name"; print "\n"; print $ref->{'job'; print "\n"; my %hash_copy = %$ref; print %hash_copy; print "\n"; steve DJ namestevejobdj exit; VI, September 2008 Page 36

19 Perl References References vioannid$./ref2.pl = ( "bruce", "michael" ); my $ref2 = \@list; print ${$ref2[0]; print "\n"; print $ref2->[1]; print "\n"; bruce michael print "\n"; brucemichael exit; VI, September 2008 Page 37 Perl Outline : Filehandles & File Tests Subroutines (functions) References passing arguments to functions nested data structure Packages/Modules Namespace/@INC VI, September 2008 Page 38

20 Perl Nested Data Structures References are commonly used in Nested Data Structures: ARRAY REF ARRAY REF Gene1 ARRAY REF Gene2 ARRAY REF AKT_signaling LCK_signaling Erk BRCA-1_pathway Integrin_signaling TCF-1_pathway VI, September 2008 Page 39 Perl Nested Data Structures References are commonly used in Nested Data Structures: = qw(akt_signaling Erk Integrin_signaling); = ('gene1', \@gene1); =qw(lck_signaling BRCA-1_pathway TCF-1_pathway ); = ('gene2', \@gene2); = (\@gene1_name,\@gene2_name,); ; print "\n"; ; print "\n"; my $value_array_gene_name_refs1 print $value_array_gene_name_refs1 ; print "\n"; my $value_array2_field3 = ${${$all_gene_names[1][1][2]; print $value_array2_field3; print "\n"; ARRAY(0x180b318)ARRAY(0x180d888) gene1array(0x180b324) gene1 TCF-1_pathway exit; VI, September 2008 Page 40

21 Perl Nested Data Structures References are commonly used in Nested Data Structures: Arrays of arrays Hashes of arrays Arrays of Hashes Hashes of hashes And more! When the nested data structures become to complex, it may be worth considering Object Oriented Perl programming VI, September 2008 Page 41 Perl script1.pl my $v1 = complex_operation (param1);... my $v2 = complex_operation (param2); script2.pl my $v1 = complex_operation (param1);... my $v2 = complex_operation (param2); exit ; exit ; sub complex_operation { sub complex_operation { VI, September 2008 Page 42

22 Perl Outline : Filehandles & File Tests Subroutines (functions) References passing arguments to functions nested data structure Packages/Modules Namespace/@INC VI, September 2008 Page 43 Perl Package/Module script1.pl use Mymod; my $v1 = Mymod::complex_operation (param1);... my $v2 = Mymod::complex_operation (param2);... script2.pl use Mymod; Module Mymod sub complex_operation { my $v1 = Mymod::complex_operation (param1);... my $v2 = Mymod::complex_operation (param2);... VI, September 2008 Page 44

23 Perl Package/Module Structure of module Mymod.pm Calling the functions in a script package Mymod; sub f { sub g = ( ); 1; use Mymod; Mymod::f($param); $a = Mymod::g(); A module is a package defined in a file whose name is the same as the package. VI, September 2008 Page 45 Perl Outline : Filehandles & File Tests Subroutines (functions) References passing arguments to functions nested data structure Packages/Modules Namespace/@INC VI, September 2008 Page 46

24 Perl namespace A namespace stores names (or identifiers), including names of variables, subroutines, filehandles, and formats. Each namespace has its own symbol table, which is basically a hash with a key for each identifier. Variables in different namespaces can even have the same name, but they are completely distinct from one another. The default namespace for programs is main. Each package starts with a package declaration. The package call takes one argument, the name of the package. Within the scope of a package declaration, all regular identifiers are created within that package (except for my variables). VI, September 2008 Page 47 / Export Perl locates modules by searching array (defined when Perl is built). When you refer to MyModule in your program, Perl searches in the directories listed for the module file MyModule.pm, and uses the first one it finds. VI, September 2008 Page 48

25 / Export To include a module in your program: require Module; use Module; The difference between use and require is that use pulls in the module at compile time. This means that functions like func1 or func2 can be used as predeclared list operators throughout the file. func1($a,$b); The require call does not necessarily load the module during compilation, so you must explicitly qualify its routines with the package name. Module::func1($a,$b); VI, September 2008 Page 49 / Export Animals.pm # two essential lines in a package require Exporter; = ('Exporter'); # inherits from Exporter Package # export by default = qw($cat %canis carnivore); # export on demand = qw($tiger); # variables & functions declaration... 1; User's script use Animals; # import symbols use Animals qw($cat $tiger); # import $tiger and $cat VI, September 2008 Page 50

26 Perl VI, September 2008 Page 51