Introduction to Perl Scott Hazelhurst - PowerPoint PPT Presentation

Introduction to Perl File operations Files in general ◮ open(DATAF, "figs.dat") read ◮ open(DATAF, "<figs.dat") read ◮ open(DATAF, ">figs.dat") write ◮ open(DATAF, ">>figs.dat") append ◮ open(DATAF, "| output-pipe-cmd"); set up output filter ◮ open(DATAF, "input-pipe-cmd| "); set up input filter

Introduction to Perl File operations Files in general ◮ open(DATAF, "figs.dat") read ◮ open(DATAF, "<figs.dat") read ◮ open(DATAF, ">figs.dat") write ◮ open(DATAF, ">>figs.dat") append ◮ open(DATAF, "| output-pipe-cmd"); set up output filter ◮ open(DATAF, "input-pipe-cmd| "); set up input filter To print to a file that is open for writing, use the related file handle in the print statement.

Introduction to Perl File operations Input from files Input from files Suppose that INP is a file handle. A reference to <INP> does the following: ◮ Returns the next line of input; ◮ Consumes the input – in the case of a file, advances the file pointer to the next line of the file. ◮ NB: end-of-line marker read in.

Introduction to Perl File operations Input from files for($i=0; $i <3; $i++) { $x=<INP >; print "**$x##" } Assuming that file contains apple , banana , cherry .

Introduction to Perl File operations Input from files for($i=0; $i <3; $i++) { $x=<INP >; print "**$x##" } Assuming that file contains apple , banana , cherry . **apple ##**banana ##**cherry ##

Introduction to Perl File operations Input from files To add up the numbers in a file with three numbers. open(INP ,"nums.txt"); $x1 = <INP >; $x2 = <INP >; $x3 = <INP >; print "Answer is " . $x1 + $x2 + $x3; or open(INP ,"nums.txt"); print "Answer is " . (<INP > + <INP > + <INP >);

Introduction to Perl File operations Input from files What’s the difference between print "Answer is " . (<INP > + <INP > + <INP >); and print "Answer is . (<INP > + <INP > + <INP >) ";

Introduction to Perl File operations Input from files Add up odd numbers in file print "Enter the file name: "; $namef = <STDIN >; open(DATAF , $namef ); while($x = <DATAF >) { if ($x % 2) { $sum = $sum + $x; } } close(DATAF ); print "The sum is $sum\n";

Introduction to Perl File operations Input from files A common Perl idiom is open(DATAF ,$namef) or die "Can’t open

Introduction to Perl File operations Implicit operands Implicit Operands Perl uses implicit operands extensively. ◮ We are told that this is a feature. ◮ The main culprit: $_ or $ARG Set (among other places) by reference to a file handle. Many operators use $ARG if not given explicit operator explicitly. ◮ The following prints out the contents of a file: while (<DATAF>) {print};

Introduction to Perl File operations Implicit operands Exercise Write a Perl program that reads integers from a file called nums.dat and counts how many numbers are ◮ less than zero ◮ between zero and 10 ◮ greater than or equal to 11 If there is no such file, your program should print an error message and halt.

Introduction to Perl Arrays/lists Arrays/lists Array variables are prefixed by @ my @days; @days = ("Sun", "Mon", "Tue", "Wed", "Thu", "F ◮ Arrays indexed from 0

Introduction to Perl Arrays/lists Arrays/lists Array variables are prefixed by @ my @days; @days = ("Sun", "Mon", "Tue", "Wed", "Thu", "F ◮ Arrays indexed from 0 ◮ Individual element are scalars: so $days[0]

Introduction to Perl Arrays/lists Common to use foreach @days = ("Sun", "Mon", "Tue", "Wed", " foreach $d (@days) { print "Day $d\n"; }

Introduction to Perl Arrays/lists Quote words Short hand for arrays of words @days = qw(Sun Mon Tue Wed Thu Fri Sat

Introduction to Perl Arrays/lists @ARGV – program’s arguments @ARGV : Predefined variable array ◮ Contains the program’s arguments – values passed by the caller. ◮ If the program is run as follows: ./example.pl apple pear 1 2 3 array @ARGV contains those values ◮ $ARGV[0] is apple ; ◮ $ARGV[3] is 2 ;

Introduction to Perl Arrays/lists Array semantics Expressions are evaluated in scalar or list context. ◮ Similar or identical expressions can evaluate to different things in different contexts.

Introduction to Perl Arrays/lists Array semantics Expressions are evaluated in scalar or list context. ◮ Similar or identical expressions can evaluate to different things in different contexts. Context determined by operation: ◮ LHS of assignment determines context ◮ Operators or functions may determine context

Introduction to Perl Arrays/lists Array context ◮ print @days yields SunMonTueWedThuFriSat ◮ @weekdays = @days[1..5] array $weekdays set to Mon .. Fri ◮ @days[1] is a one element array

Introduction to Perl Arrays/lists Array context ◮ print @days yields SunMonTueWedThuFriSat ◮ @weekdays = @days[1..5] array $weekdays set to Mon .. Fri ◮ @days[1] is a one element array Scalar context ◮ $numdays = @days; sets $numdays to 7

Introduction to Perl Arrays/lists Array context ◮ print @days yields SunMonTueWedThuFriSat ◮ @weekdays = @days[1..5] array $weekdays set to Mon .. Fri ◮ @days[1] is a one element array Scalar context ◮ $numdays = @days; sets $numdays to 7 ◮ $y = ("Sun","Mon","Tue","Wed","Thu","Fri","Sat") sets $y to Sat

Introduction to Perl Arrays/lists Array context ◮ print @days yields SunMonTueWedThuFriSat ◮ @weekdays = @days[1..5] array $weekdays set to Mon .. Fri ◮ @days[1] is a one element array Scalar context ◮ $numdays = @days; sets $numdays to 7 ◮ $y = ("Sun","Mon","Tue","Wed","Thu","Fri","Sat") sets $y to Sat ◮ $weekdays = $days[1..5] sets $weekdays to 5 ◮ $#days is 6 – the highest index of @days

Introduction to Perl Arrays/lists Useful functions ◮ push : adds something to the right of the array ◮ pop : removes the rightmost element of the array. ◮ shift/unshift ◮ sort: returns a sorted list by default string order ascending, but can be changed.

Introduction to Perl Arrays/lists Arrays are inherently 1D ◮ Need references to handle multi-dimensional arrays

Introduction to Perl Arrays/lists Asides Asides on strings ◮ splitting @x = split ";", "1;2;3"; foreach $s (@x) { print "$s\n"; } ◮ chop , chomp . ◮ see regexes later

Introduction to Perl Hash tables Hash tables Unordered set of scalars which allows fast information retrieval: ◮ Elements accessed/indexed by a string value associated with it ◮ Variables prefixed by a %, e.g. %currency ◮ Individual elements are scalar: $currency["South Africa"]

Introduction to Perl Hash tables $currency["South Africa"]="ZAR"; $currency["Britain"] = "GBP";

Introduction to Perl Hash tables Example %day2num = ("Sun",0, "Mon",1, "Tue",2, "Wed",3, "Thu",4, "Fri",5, "Sat",6) Better is %day2num= ("Sun"=>0, "Mon"=>1, "Tue"=>2, "Wed"=>3, "Thu"=>4, "Fri"=>5, "Sat"=>6) Referred to as $day2num{"Wed"}

Introduction to Perl Hash tables Useful hash operations ◮ keys returns list of keys in hash table. Order non-deterministic.

Introduction to Perl Hash tables Useful hash operations ◮ keys returns list of keys in hash table. Order non-deterministic. ◮ values returns list values stored in the hash table. Order of no significance.

Introduction to Perl Hash tables Useful hash operations ◮ keys returns list of keys in hash table. Order non-deterministic. ◮ values returns list values stored in the hash table. Order of no significance. ◮ sort keys %table lists the keys in lexicographic order

Introduction to Perl Hash tables Example # read in from file while ($name = <INP>) { $reg = <INP>; $carreg{$name} = $reg; } # print out in order of name foreach $n (sort keys %carreg) { print "Car reg of $n is $carreg{$n} \n"; }

Introduction to Perl Hash tables Can also tell sort how to sort: ◮ sort {$a <=> $b} list sorts the list in numeric order. ◮ sort {$table{$a} cmp $table{$b}} keys %table sorts the keys so that corresponding hash table elements are in order

Introduction to Perl Hash tables #print out in order of car reg foreach $n (sort {$carreg{$a} cmp $carreg{$b}} keys %carreg) { print "$carreg{$n} owned by $n\n"; }

Introduction to Perl Procedures Procedures Perl has procedures but its parameter passing mechanism is poor. ◮ Suppose we have a procedure plus that adds up two numbers. Called: $x = &plus($a, $b); where $a and $b are the parameters. Call by value semantics

Introduction to Perl Procedures Declaring a subroutine To declare a subroutine: sub NAME BLOCK e.g. sub printhead { print "Name Age Number Balance\n"; } ... &printhead();

Introduction to Perl Procedures Parameters Procedures have one formal parameter: @_ ◮ The values of the actual parameter are given to the formal parameter (call-by-value). ◮ @_ : a list local to the procedure. sub plus { sub plus { $x = $_[0]; my ($x,$y) = @_; $y = $_[1]; return $x+$y; return $x + $y; } }

Introduction to Perl Procedures A common idiom uses shift sub plus { $x = shift @_; $y = shift @_; return $x + $y; }

Introduction to Perl Procedures Example A procedure to add up a list: sub addlist {$sum = 0; foreach $num (@_) {$sum += $num}; return $sum;} sub proclist { my ($f1,$f2,@nums) = @_; foreach $n (@nums) {$sum = $sum+$n; } return ($f1*$f2*$sum); } $x = &addlist(1,2,3,5,6,9); $y = &proclist(3,4,1,1,0,2);

Introduction to Perl Procedures The following does not work (s sub dotprod { (@a,@b) = @_; ... ... } @x = (1,2,3); @y = (4,5,6); &dotprod(@x,@y);

Introduction to Perl Procedures ◮ Formal parameter is an unstructured list (possible danger in passing multiple lists as parameters) ◮ Forward declarations: sub addlist; Telling Perl that addlist is a procedure which will be declared elsewhere. ◮ Can have anonymous procedures that get assigned to variables. ◮ Weakness in parameter system can be overcome by using references. ◮ Default: all variables are global wherever defined. This is even recognised by the Perl community to be a Bad Thing Declare variables local inside procedures. Best way : prefix first use of variable in a procedure with with my. Lexical scoping.

Introduction to Perl References References References are mechanisms for a variable to refer to something, e.g. (1) another variable; (2) a piece of data; (3); a function Symbolic references Can turn a string into a variable $x = 123; $y = "x"; $$y = 5; print $x;

Introduction to Perl References Hard references Can use the \ operator to dereference a variable, and -> to dereference. @a = (10,20,30,40,50); $x = \@a; for $e ( @{$x} ) { print "$e\n"; } print $x->[0];

Introduction to Perl References Call by reference sub count { my ($fname , $rcount) = @_; chomp $fname; unless (-T $fname) { return; } open(FINP ,$fname ); while (<FINP >) { $$rcount ++ } close(FINP ); }

Introduction to Perl References @files = ‘ls -1 $ARGV [0]‘; $n = 0; for $f (@files) { &count($f ,\$n); } print "Total number of lines is $n\n";

Introduction to Perl References Passing multiple arrays sub dotprod { ($a,$b)=@_; .... } @x = (1,2,3); @y = (4,5,6); &dotprod(\@x,\@y); Note that only scalars are passed.

Introduction to Perl References Refs to anonymous arrays and hashes Square brackets creates an array – returns a reference $a = [ 10, 20, 30, 40]; ◮ Error: @a = [ 10, 20, 30, 40]; Curly braces creates a hash – returns a reference $day = {"sun"=>0, "mon"=>1, "tues"=> .....}

Introduction to Perl Modules Modules A module is a collection of code, data structures that can be used as a library ◮ Often see it in OO programming Magic word is use use IO; ◮ To access something is in a module use :: . So, module::thing ◮ Modules can be nested.

Introduction to Perl Modules Example use IO:: Compress :: Bzip2; IO:: Compress :: Bzip2 :: bzip2 ("do.pl", "do.pl.bz

Introduction to Perl Modules Example use IO:: Compress :: Bzip2; IO:: Compress :: Bzip2 :: bzip2 ("do.pl", "do.pl.bz Can also import specific things use IO:: Compress :: Bzip2 qw(bzip2 $Bzip2Error ); unless (bzip2 ("do.plx", "do.pl.bz2")) { warn "Compression failed returning : $Bzip2 }

Introduction to Perl Objects Objects Data structures which ◮ contain data, know functions that can apply to them; ◮ anonymous ◮ accessed through references ◮ typically organised in classes

Introduction to Perl Objects use Bio::Seq; $seqio = Bio::SeqIO ->new(’-format ’ => ’embl ’ , -file $seqobj = $seqio ->next_seq (); $seqstr = $seqobj ->seq (); $seqstr = $seqobj ->subseq (10 ,50); @features = $seqobj -> get_SeqFeatures (); foreach my $feat ( @features ) { print "Feature ",$feat ->primary_tag , " starts ",$feat ->start , " ends ", $feat ->end ," strand ",$feat ->strand ,"\n"; }

Introduction to Perl Regular expressions Regular expressions, matching, and more Perl’s regular expression support powerful ◮ concise way of describing a set of strings. Typical: a command uses a regular expression to process some argument. ◮ Example: split uses a regex to split a string $line = "Gauteng;Johannesburg GP 7"; @info = split("[ ;]", $line); ($prov, $capital,$reg, $pop) = split("[ ;] ", $line);

Introduction to Perl Regular expressions Specifying Regular Expressions ◮ Most characters stand for themselves: F Fred 6312

Introduction to Perl Regular expressions Specifying Regular Expressions ◮ Most characters stand for themselves: F Fred 6312 ◮ \ | ( ) [ { ^ $ * + ? . are metacharacters (have special meaning) ◮ escape with a backslash for the chars: Fred stands for the string (Fred)

Introduction to Perl Regular expressions Specifying Regular Expressions ◮ Most characters stand for themselves: F Fred 6312 ◮ \ | ( ) [ { ^ $ * + ? . are metacharacters (have special meaning) ◮ escape with a backslash for the chars: Fred stands for the string (Fred) ◮ To group things together, use parentheses.

Introduction to Perl Regular expressions Specifying Regular Expressions ◮ Most characters stand for themselves: F Fred 6312 ◮ \ | ( ) [ { ^ $ * + ? . are metacharacters (have special meaning) ◮ escape with a backslash for the chars: Fred stands for the string (Fred) ◮ To group things together, use parentheses. ◮ To specify alternatives, use | (green|red) apples stands for green apples or red apples

Introduction to Perl Regular expressions Specifying Regular Expressions ◮ Most characters stand for themselves: F Fred 6312 ◮ \ | ( ) [ { ^ $ * + ? . are metacharacters (have special meaning) ◮ escape with a backslash for the chars: Fred stands for the string (Fred) ◮ To group things together, use parentheses. ◮ To specify alternatives, use | (green|red) apples stands for green apples or red apples

Introduction to Perl Regular expressions Specifying Regular Expressions ◮ A list of characters in square brackets matches any of the characters. ◮ [YyNn] matches any of an upper or lower case “y” or “n”. ◮ [A-Za-z0-9] is all the alphanumeric characters

Introduction to Perl Regular expressions ◮ \n new line; \t tab; \s a whitespace;

Introduction to Perl Regular expressions ◮ \n new line; \t tab; \s a whitespace; ◮ \d digit; \D non-digit;

Introduction to Perl Regular expressions ◮ \n new line; \t tab; \s a whitespace; ◮ \d digit; \D non-digit; ◮ \w a word charater, \W a non-word character

Introduction to Perl Regular expressions ◮ \n new line; \t tab; \s a whitespace; ◮ \d digit; \D non-digit; ◮ \w a word charater, \W a non-word character ◮ . anything but a \n