Introduction to perl

Introduction to perlIntroduction to perl

Research Computing/Larry MasonFebruary 17, 2009

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Class MaterialClass Material

Point web browser to:

http://its.unc.edu/Research

Click on “Training” (in left column)

Click on “ITS Research Computing Training Presentations” (Bottom paragraph)

Click on “Getting Started on Perl” (under General Computing)

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ssh to linux hostssh to linux host

To start ssh using SecureCRT in Windows:

Start Programs [Remote Services] SecureCRT

Click the Quick Connect icon at the top. (Second icon from left?)

Hostname: emerald.isis.unc.edu

Login with your ONYEN and password

Create a directory for this course

mkdir perl_intro [or other name of your choice]

cd perl_intro

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Bring in class filesBring in class files

On the linux host (emerald?) in perl_intro:

cp /afs/isis/depts/its/public_html/divisions/rc/training/scientific/perl_Intro/examples/* .

ls –l

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Running perl scriptsRunning perl scripts

ls –l 001hello.pl

Shows permissions in left column

-rwxr-xr-x means the script can be run by everybody (the “x” means “executable”)

chmod 700 *.pl

To make all perl scripts runable / executable by you, the owner

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#!/afs/isis/pkg/isis/bin/perl –wprint STDOUT “Hello, world.”;

print STDOUT “Hello, world.\n”;

print STDOUT ‘Hello, world.\n’;

print STDOUT “\n\n”;

1) Hello, World!1) Hello, World!

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2) Various Variables2) Various Variables

#!/afs/isis/pkg/isis/bin/perl –w

$string = “Hello,” . “ world.\n”; # concatenation

print STDOUT “$string”;

$number = 2009;

print STDOUT “the number is $number\n”;

$number[0] = “one”;

$number[1] = “2”;

$number[2] = “three”;

print STDOUT “@number\n”;

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3) pragmas3) pragmas


use strict;

my $string = “/tmp/fileout.$$”;

my @number;

…

# Note the error messages.

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4) Variable flexibility4) Variable flexibility


use strict;

my $file = “/tmp/fileout.$$”;

my $string = “Hello, world”;

…

$number[0] = 14;

print STDOUT “$number[0]\n”;

$number[0] = substr($string,0,5);


exit;

…

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5) String or Number5) String or Number


…

my $string = “123456789”;

…

$number[0] = substr($string,-5,3);


print STDOUT “$string\n”;

$number[0] = $string * 3;


$string = “abc”; $number[0] = $string * 3;


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6) Files: in and out6) Files: in and out


my $string = “/tmp/fileout.$$”;

my $number = 2009; my $record = “”;

my @number = (“one”, “2”, “three”);

open OUTFILE, “>$string”;

print OUTFILE “$number\nnumber[1] is $number[1]\nnumber[2] is

$number[2]\n\nOUTFILE is $string”;

close OUTFILE;

open SAM, “<$string”;

$record = <SAM>;

print STDOUT “$record”;

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7) Loops: while7) Loops: while


. . .


while (<SAM>) {

print STDOUT “$_”;

}

close SAM;

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8) chop and chomp8) chop and chomp


. . .


while (<SAM>) {


chomp $_;


chop $_;


}

# close of SAM unnecessary here because program ends here

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9)Loops: for9)Loops: for


...

my $last = $#number;

for ($i = 0; $i <= $last; $i++) {

print OUTFILE “$number[$i]\n”;

} # end for each element of the @number array

close OUTFILE;

open SAM,”<$string”;

while (<SAM>) {


} # end while records from file SAM

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10) Next10) Next


my $count = 0;

…

close ANYFILE;

open ANYFILE, “<$file”;

while (<ANYFILE>) {

chomp $_; $count++;

if ( $_ gt “one” ) { next; }

print STDOUT “now count is $count\n”;

} # end while ANYFILE records

print STDOUT “Final count is $count\n”;

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11) Last11) Last


…

CASE: while (<ANYFILE>) { chomp $_; $count++

if ( $_ eq “two” ) { next CASE;}

elsif ( $_ ne “one” ) {

print STDOUT “What\’s $_ doing here?\n”;

last; }

else { print STDOUT “It\’s only $_\n”;

} # end else found a one

print STDOUT “Record number $count is $_\n”;

} # end while ANYFILE records

print STDOUT “Final count is $count\n”;

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12) hashes12) hashes


my $var = “rosebud”;

my %number;

$number{one} = “one”;

$number{‘two’} = “something”;

$number{“molly”} = 3;

$number{$var} = “4”;

print STDOUT “%number\n”;

print STDOUT “$number{molly} and $number{rosebud}\n”;

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13)loops: foreach13)loops: foreach


…

my $var = “”;

my %number = (‘one’,1,’two’,2,’molly’,3,’rosebud’,4);

open ANYFILE, “>$string”;

foreach $var ( keys %number ) {

print ANYFILE “$number{$var}\n”;

} # end foreach index key of %number


# check the contents of the output file $string

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Functions: subFunctions: sub

$result = &mysub ($param);

sub mysub {

my $something = $_[0];

return;

}

Could use “return $something;” with the same result.

Value of last expression evaluated is returned by default.

Parameters are passed to the subroutine in the array @_

Changing $_[0] would change the value of $param .

Subroutine has access to global variables.

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14) sorting14) sorting


…

open ANYFILE, “>$string”;

foreach $var ( sort keys %number ) {


} # end foreach sorted index key of %number


# what did it sort by?

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15) sorting by Value15) sorting by Value


…

sub byvalue { $number{$a} <=> $number{$b}; }

open ANYFILE, “$string”;

foreach $var ( sort byvalue keys %number ) {


} # end foreach index, sorted by value, keys of %number


# Now check the sequence of records in $string

# sub byvalue { $number{$b} <=> $number{$a}; }

# sub byvalue { $number{$a} cmp $number{$b}; }

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16) Command Input16) Command Input


…

$file = “/tmp/fileout\*”;

$string = `/usr/bin/wc $file`; # all in one string

@number = `/usr/bin/wc $file`; # each record one element

print STDOUT “STRING is $string\n”;

print STDOUT “NUMBER STUFF\n@number\n”;

exit;

…

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17) More Command Input

17) More Command Input


...

my $var = “”;

my $file = “/tmp/fileout\*”;

$var = “/bin/ls $file”;

open LS, “$var |”;

while (<LS>) {


} # end while ls command output

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18) Parsing Input18) Parsing Input


…

my @F;

@number = `/usr/bin/wc $file`;

print STDOUT “INPUT $number[0]\n”;

@F = split(‘ ‘,$number[$count]);

print STDOUT “ALL F[0] $F[0] F[2] $F[2] F[4] $F[4]\n”;

@F = split(‘ ‘,$number[$count],3);

print STDOUT “THREE F[0] $F[0] F[2] $F[2]\n”;

$#F = 1;

print STDOUT “Array of two F[0] $F[0] F[2] $F[2]\n”;

exit;

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19) More Parsing19) More Parsing


…

my $this = my $that = my $trash =0;

print STDOUT “INPUT $number[0]\n”;

$#F = -1;

print STDOUT “F[0] $F[0]\n”;

@F = split(/\//,$number[0]);

print STDOUT “F[0] $F[0] F[1] $F[1] F[2] $F[2]\n”;

($this, $that, $trash) = split(/tmp/,$number[0],3);

print STDOUT “this $this that $that trash $trash\n”;

exit;

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Functions:Pattern Matching

Functions:Pattern Matching

m/PATTERN/gimosx

m#PATTERN#gimosx

metacharacters \ | ( ) [ { ^ $ * + ? .

“^” matches beginning of string

“$” matches end of string

“\n” newline character

“\t” tab character

“\d” digit (0-9)

“\D” non-digit

“\s” whitespace character

“\S” non-whitespace chatacter

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20) Regular Expressions II

20) Regular Expressions II


my $one = my $five = my $fifteen = 0;

($one, $five, $fifteen) = (`/usr/bin/uptime` =~ /(\d+\.\d+)/g);

print STDOUT “one is $one, five is $five, fifteen is $fifteen\n”;

my $paragraph = “”; my $sentences = 0;

$/ = “”;

while ($paragraph = <>) {

while ($paragraph =~ /[a-z][‘”)]*[.!?]+[‘”)]*\s/g) {

$sentences++;

} }

print STDOUT “$sentences\n”;

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Functions: dieFunctions: die

open OUTFILE, “>$file” or die;

open OUTFILE, “>$file” or die “Could not open $file, stopped “;

Perl will add “at [pgmname] line [N].” to the die output.

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21) Functions: getpwent

21) Functions: getpwent


my $name = my $passwd = my $uid = $gid = “”;

my $quota = my $comment = my $gcos = “”;

my $dir = my $shell = “”; my %uid;

($name, $passwd, $unid, $gid, $quota, $comment, $gcos, $dir,

$shell) = getpwent;

print STDOUT “name = $name and shell = $shell\n”;

while (($name, $passwd, $uid) = getpwent) {

$uid{$name} = $uid; # add to hash

} # end while records in /etc/passwd

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22) Functions: index , length

22) Functions: index , length


my $here = my $position = 0;

my $string = “abcdefghi”;

my $substr = “def”;

$here = index ($string, $substr, $position);

print STDOUT “$substr is at position $here in $string\n”;

$here = length ($string);

print STDOUT “The string is $here in length.\n”;

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23) Functions: time23) Functions: time

my $second = my $min = my $hour = my $mday = my $mon = 0;

my $year = my $wday = my $yday = my $isdst = 0;

($second, $min, $hour, $mday, $mon, $year, $wday, $yday, $isdst)

= localtime (time);

January is month “0”.

The year needs 1900 added to it.

Sunday is wday “0”.

Is Daylight Savings Time is zero for EST.

“time” returns the seconds since the Epoch.

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Various functionsVarious functions

sleep 60; # wait for 60 seconds before going on.

system “$command”; # executes the string in $command

# in a forked bourne shell and waits for it to finish.

tr/[searchlist/replacementlist/cds;

$result =~ tr/A-Z/a-z/; # Translates the string in $result

# uppercase letters changed to lower case.

# output stored in $result.

# “c” after “///” means to compliment the searchlist

# “d” means delete characters not replaced

# “s” means print only one of a sequence all the same

undef @F; undef %H; undef $string; # undefines things.

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Modules: exampleModules: example

use strict; use Getopt::Std;

use vars qw($opt_u, $opt_r, $opt_s, $opt_g);

getopts(‘u:rsg:’);

# colon means parameters “u” and “g” have arguments.

# each causes a variable with name “$opt_” prefix.

# If r is used the $opt_r variable will be “1”, else “0”.

# The “use vars” is a “pragma” that allows this to work with

# use strict.

# the “qw” is “quote words” and is a way to present a list.

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The EndThe End

Introduction to perl

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