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PERL

PERL. The Scripting Programming Language. #!/usr/bin/perl. 1. WHAT IS PERL ?. Perl is a programming language. Unlike programming languages such as C and Fortran, Perl programs are scripts which direct the execution of the program “perl”.

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PERL

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  1. PERL The Scripting Programming Language

  2. #!/usr/bin/perl 1 WHAT IS PERL ? • Perl is a programming language. • Unlike programming languages such as C and Fortran, Perl programs are scripts which direct the execution of the program “perl”. • Perl execution is similar in form to shell script execution. • Look at the introduction: • http://perldoc.perl.org/perlintro.html

  3. #!/usr/bin/perl 2 WHY USE PERL ? • Perl is quick and easy to write. • Perl is versatile: • File/Sequence Management • Command Line Execution • Database • GUI • Webpage • Easy manipulation of sequences in genetic sequence analysis

  4. #!/usr/bin/perl 3 BASIC SCRIPT • The script “Example.pl” is: • #!/usr/bin/perl • $x = 1; • $y = 1; • $z = $x + $y; • print “$x + $y = $z”; • The execution of Example.pl is: > chmod +x Example.pl > ./Example.pl 1 + 1 = 2

  5. #!/usr/bin/perl 4 WHAT ARE PERL VARIABLES ? • Three main perl variables: • Scalar : $name • Array : @name • Hash : %name

  6. #!/usr/bin/perl 5 PERL SCALAR • Scalar variables are common and versatile. • Scalar variables hold either numbers or strings • $number = 12.4; • $string = “Value is: “; • print “$string$number\n”; • $string = $string . “number 12”; • print “$string\n”; • Generates: • Value is: 12.4 • Value is: number 12

  7. #!/usr/bin/perl 6 PERL ARRAY • Array holds a list of values • $value = “there”; • @array = (“Hello”,$value,1); • print “$arr[0] $arr[1] number $arr[2]\n”; • $array[2] = 2; • $array[3] = “again”; • print “$arr[0] $arr[3] number “, $arr[2] – 1, “\n”; • $size = @array; • print “Array has size $size\n”; • Generates: • Hello there number 1 • Hello again number 1 • Array has size 4

  8. #!/usr/bin/perl 7 PERL HASH • Hash holds references to values • %hash = ( “number” => 1, 34 => “Hello there” ); • print $hash{34}, “ number “, $hash{“number”}, “\n”; • @array = keys %hash; • foreach $ref (@array){ • print “Key: $ref = $hash{$ref}\n”; • } • Generates: • Hello there number 1 • Key number = 1 • Key 34 = Hello there

  9. #!/usr/bin/perl 8 LINE CONTROL • Perl controls line execution with • if – elsif – else • while • for • foreach • With comparisons: • For numbers: • < (less than), > (greater than) • <= (less than or equal), >= (greater than or equal) • == (equal) • For strings: • eq (equal strings) • ne (not equal strings)

  10. #!/usr/bin/perl 9 IF – ELSIF - ELSE • For example: • if( $val < 2 ){ • print “Value is less than 2\n”; • } • elsif( $val == 2 ){ • print “Value is equal to 2\n”; • } • else{ • print “Value is greater than 2\n”; • } • if( $stringA eq $stringB ){ • print “Both strings are the same\n”; • } • else{ • print “Both strings are different\n”; • }

  11. #!/usr/bin/perl 10 WHILE, FOR LOOPS • For example: • # while( condition ) • while( $i < 20 ){ • print “The value $i is less than 20\n”; • $i++; • } • # for( initial operation; condition; loop action ) • for( $i = 0; $i < 20; $i++ ){ • print “The value $i is greater or equal to 0\n”; • print “The value $i is less than 20\n”; • }

  12. #!/usr/bin/perl 11 FOREACH LOOP • For example: • # foreach $value ( @array ) • foreach $value ( @array ){ • print “The value $value is in the array\n”; • } • foreach $value ( keys %hash ){ • print “$value has value $hash{$value}\n”; • } • Note that foreach loops traverse the array from low index to high index.

  13. #!/usr/bin/perl 12 READING IN DATA • Array @ARGV holds command line arguments • To open and read in a file: • open(IN,”$fileName”); • $firstLine = <IN>; • while(<IN>){ • print $_; • } • close(IN); • To write to a file: • open(OUT,”> $fileName”); • print OUT “Write this into $fileName\n”; • close(OUT);

  14. #!/usr/bin/perl 13 STANDARD STREAMS • To read standard input: • print “Write something: “; • $value = <STDIN>; • print “User wrote $value\n”; • To write to standard output: • print STDOUT “You see this on the command line\n”; • To write to standard error: • print STDERR “This is written as an error\n”;

  15. #!/usr/bin/perl 14 REGULAR EXPRESIONS • Regular expressions are a powerful tool for locating and modifying data • The basic evaluation of regular expression are written as: • $variable =~ /regular expression/ • which returns true if the variable holds to the regular expression and false otherwise.

  16. #!/usr/bin/perl 15 REG EXP EXAMPLES • Example: • if( $string =~ /Jonathan/ ){ • print “The string contains Jonathan”; • print “as a substring.\n”; • } • if( $string !~ /Myers/ ){ • print “The string does not contain”; • print “Myers as a substring”; • }

  17. #!/usr/bin/perl 16 REG EXP Variables • Basic elements in regular expressions: • /./ = Any single character • /\w/ = Any character a-z, A-Z, 0-9, and ‘_’ • /\d/ = Any digit 0-9 • /\s/ = space, tab, or enter • /\./ = The character ‘.’ • /\\/ = The character ‘\’ • Definition of groups: • /[xyz]/ = Occurrence of either x, y or z • /[^xyz]/ = Occurrence of anything but x, y, or z • Location of occurrence: • /^x/ = Occurrence of x as the first character • /x$/ = Occurrence of x as the last character

  18. #!/usr/bin/perl 17 REG EXP Counts • Number of occurrences: • /x*/ = 0 or more copies of character ‘x’ in a row • /x+/ = 1 or more copies of character ‘x’ in a row • /x{3}/ = 3 copies of character ‘x’ in a row • /(str)*/ = 0 or more copies of string ‘str’ in a row • /$var*/ = 0 or more copies of the string $var in a row • Example: • $str = “a string with too much”; • if( $str =~ /o{2}/ ){ • print “True!\n”; • } • if( $str =~ /(crazy)*/ ){ • print “True!\n”; • }

  19. #!/usr/bin/perl 18 Substitutions • Substitutions are regular expressions that define replacements within strings. • $str =~ s/(regular expression)/(replacement)/ • Examples: • $str = “aabbccddeeff”; • $str =~ s/c/1/; • print “$str\n”; • $str =~ s/.$/2/; • print “$str\n”; • $str =~ s/^\w{3}/start /; • print “$str\n”; • Generates: • aabb1cddeeff • aabb1cddeef2 • start b1cddeef2

  20. #!/usr/bin/perl 19 SPLIT FUNCTION • Split function breaks a string into an array of strings • @array = split(/(regular expression)/,$string) • Example: • $str = “A set of strings”; • @array = split(/\s+/,$str); • for( $i = 0; $i < @array; $i++ ){ • print “$array[$i]\n”; • } • Generates: • A • set • of • strings

  21. #!/usr/bin/perl 20 REMEMBER PRACTICE!!!! • We learn by doing !!!! • Look at these sites!!! • http://perldoc.perl.org/perlintro.html • http://www.perl.com/pub/a/2000/10/begperl1.html • http://www.comp.leeds.ac.uk/Perl/start.html

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