Lecture 4

0. Why scripting
1. Perl scripts
2. Scalar Data
3. Lists and arrays
4. Input Output
5. Regular Expressions

We won’t talk about subroutines etc.

A good reference:

https://learn.perl.org/books/beginning-perl/

Figure below is from a recent paper I wrote, there are 150 computations in each picture (one for each marker) and there is probably around 20 figures in the paper. So a total of 3000 setups using different parameters.

If each setup takes 30 seconds to change, save compile and start the run, the setup time is 25h!

• Run a simulation using 1,2,3,… number of gridpoints.
• Format the output of a simulation.
• Produce a latex table from data.
• Do it all at once.
• Launch multiple simulations at once.

A simple hello.pl would be

#!/usr/apps/bin/perl

print "Hello World!\n";

The first line dictates which version of perl to use (this location is for Mac) but you could also write

#!perl

print "Hello World!\n";

if perl is in your search path.

Run it with $ perl hello.pl

• A scalar is the most fundamental type in perl and is typically a number, like 12 or 13.1, or a string, like Hello.
• Internally these are the same and a number is always a double precision floating point number.
• Literal numbers and strings are written directly into the code, e.g. Hello World!\n in the above example.
• Number literals can be integers: 123, 12 or floating point numbers: 1.2, -1.23e-3.
• The numeric operators are the usual: + - / *. Exponentiation is by **.
• For example 2**3 is the same as 8.

Single Quotes

A single quote string literal is just a collection of characters which mean exactly what they are except for \' and \\.

print 'Apa' . "\n" ;
print 'Apan\'s' . "\n" ;
print 'Apan\\' . "\n" ;

$ perl test.pl
Apa
Apan's
Apan\
$

Full stop concatenates strings.

Double Quotes

A double quote string literal a bit different in that it interpolates variables and supports backslash escapes

$q = 123;
print "A\tB\n\LBCDE\E\n$q\n";

$ perl test.pl
A       B
bcde
123
$

Here \t is tab, \n is newline \LSTUFF\E forces lowercase
$n is a variable with a value 123

Perl automatically converts between numbers and strings depending on what operator is used.

print "A" . 3*2*1 . "\n";

$ perl test.pl
A6
$

Note that * takes precedence of the concatenation operator .

A scalar variable is denoted by $name and holds a single scalar value. Scalar variables can be changed throughout the program.

$number = 123;
$name = 'Daniel';

They can also be modified with binary assignment operators like *=, =+ or .=

$sum = 0;
$sum += $number;   # $sum is now  123
$name .= 'Appelo'; # $name is now Daniel Appelo

Note that variable names are case sensitive.

• A list is an ordered array of scalars.
• An array is a variable holding a list.
• The list is the data the array the variable.
• An array is named @array_name.

@my_array = (1, 2, 3);
print $my_array[0] . "\n" ;
print $my_array[1] . "\n" ;
print $my_array[2] . "\n" ;

Note that you access the elements in the array with $ and [ ] (starting at 0.)

You can loop over all the elements in the array using foreach

@my_array = qw/ spam sausage ham/ ;
foreach $elem (@my_array) {
  print "We have $elem for lunch \n";
}

>>>
We have spam for lunch
We have sausage for lunch
We have ham for lunch

Form many control structures you may leave out $elem, then perl uses the default variable $_

@my_array = qw/ spam sausage ham/ ;
foreach (@my_array) {
  print "We have ";
  print ;
  print " for lunch \n";
}

Here both foreach and print use $_.

• Filehandles are usually ALLCAPS.
• To read from a file use “<”, to write “>” and to append “>>”.

$cmdFile="./newtonS.f90.Template";
$outFile="./newtonS.f90";
open FILE, "$cmdFile";
open OUTFILE, ">", "$outFile";

Slightly different version halting the program if the file failed to open.

$cmdFile="./newtonS.f90.Template";
$outFile="./newtonS.f90";
open(FILE,"$cmdFile") || die "cannot open file $cmdFile!" ;
open(OUTFILE,"> $outFile") || die "cannot open file!" ;

This snippet copies the file $cmdFile to $outFile.

open(FILE,"$cmdFile") || die "cannot open file $cmdFile!" ;
open(OUTFILE,"> $outFile") || die "cannot open file!" ;
while( $line = <FILE> )  # read one line at a time until EOF
{
    print OUTFILE $line;
    print $line;
}
close( OUTFILE );
close( FILE );

A typical thing to do is to search a file for some pattern and then do something (e.g. replace it with something else.) This is what perl is really good at, mainly due to it’s strong support for regular expressions or regex for short.

In short a regex is just a pattern that can be used to match a string against. Either it matches or it does not.

For example if the default $_ = "The grass is green" `` is set then if we match against the regex ``/re/

if(/re/){
  print "Found it!\n";
}

would print Found it!.

The regex \re\ is not very advanced. This is not typical ;-) Usually regexs can be very hard to read due to all the different options that can be used to construct them. A couple of options are:

• /./ - Any single character except newline.
• /X*/ - Match the preceding item X zero or more times. Thus .* matches any old junk.
• /X+/ - Match the preceding item X one or more times. E.g. /Q+/ matches Q, QQ etc.
• Parenthesis (grouping) can be used if you want to construct an item longer than one character, e.g. /(OMG)+/ would match OMGOMGOMG while /OMG+/ would match OMGGGGGGGGG.

• Modifiers can be placed after the regex to modify the pattern, /(OMG)+/i would make the match case-insensitive so that it would also match oMgomGomg.There are more of these, you can find info online.
• Anchors \b can be very useful, they ensure you “match whole word only”, e.g. /\bOMG\b/ only matches OMG and not ROMG.

You don’t have to match against the default variable just use the binding operator =~ to match against the sting on the left

$str = 'A cat in a hat';
if($str =~ /cat/){
  print "Found a cat!\n";
}

Often you want to find a pattern in a string and change it. The substitution, s///, is very useful for this! You can of course do this for the default or by using binding.

$_ = "A red rose.\n";
s/red/RED/;
print ;

>> A RED rose.

 $str = "Sju skonsjungande sjukskoterskor skotte sjuttiosju
 sjosjuka sjoman pa skeppet.\n";
$str =~ s/sjo/lake/g;
$str =~ s/sjuk/sick/g;
print $str;

>> Sju skonsjungande sickskoterskor skotte sjuttiosju lakesicka
lakeman pa skeppet.