A primer on Perl programming First structures (with examples)

A primer on Perl programming

First structures (with examples)

http://www.shlomifish.org/lecture/Perl/Newbies/lecture1/

A primer on Perl programming

Thanks for using the blog

A primer on Perl programming

Thanks for using the blog

A primer on Perl programming

• Perl is popular among bioinformaticists because it’s easy, has a huge amount of modules and was born to parse text.

• A program takes an input and returns some elaborated output.

• We need to: test conditions, and iterate blocks of instructions.

A primer on Perl programming

To reverse complement a multifasta file we need to:

•Input: filename•Open the file and parse it (headers, sequences)

• E.g.: IF line starts with ‘>’ it’s a header (one line), else concatenate lines…

•Output: Print header as is, reverse and complement the sequence

Recall: variables

$scalar contains a single value (number or string

@array is an ordered list of scalars %hash is a unordered list of values with a

name (“key”). %age = ('Andrea' => 29, 'Cesare' => 80); $age{'Carlo'} = 39; print “$name is $age{$name} old.\n”;

The foreach cycle

Performs a block of instruction for each element of an array

@names = ('Aldo', 'John', 'Jack');

foreach $name (@names) {

$count++;

print “Hello $name!\n”;

}

print “There were $count people in the array!\n”;

The for cycle

When you have to repeat a set of instruction a defined number of times.

for (initial condition; until; ending instuction ) {

...block...

}

for ($i = 1; $i<=10; $i++) {

print “\$i now is $i\n”;

}

Iterations

#print numbers 1-10 in three different ways

$i = 1;

while ($i<=10) {

print "$i\n";

$i++;

}

for ($i=1; $i<=10; $i++) {

print "$i\n";

}

foreach $i (1,2,3,4,5,6,7,8,9,10) {

print "$i\n";

}

Logical operators

They are different for numbers and strings!!!

Equal: == or eq $a == 10 $a eq 'hello'

Not equal: != or ne Greater than: >, >= Less than: <, <=

Operators

• Same precedence as in math

• +, -, *, /

• Modulus (division remainder): %

• Power: **

• Concatenate strings: .

$seqlength = 18;

print ‘There are ’.$seqlength**4.‘ combinations\n’;

Math functions

• Some functions:

• abs($x): absolute value

• int($x): integer part

• rand($x): random number up to $x

• sqrt($x): square root

$percentage = int(100*$done/$todo);

$dice = int(1+rand(6));

String functions

• Simple as:$length = length(‘Put a string here’);

• Less simple as:$portion = substr($string, $start, $length);

@pieces = split(/;/, $string);

• A world apart:

Pattern matching$string=~/TATA/;

If statement

Executes a block of code if a condition is TRUE. You can use boolean logic (and, or).

Quite simple:if (length($a) == 10) {

print “Yes, its ten characters long!\n”;

} else {

print “No, \$a is not as long as I want.\n”;

}

IF… ELSE…

Only one condition:if (condition) {

block…

} else {

block…

}

Multiple conditions: elsif (other condition)

Talking to scripts

Parameters passed from command line are stored in @ARGV (uppercase!)

Eg:$ perl myscript.pl 100 Genomics

print “First parameter: $ARGV[0]\n”;

print “Last one: GUESS\n”;

Can you write a script that prints the number of parameters passed by the users plus a list of them?

Reading a file

open(NAME, “Filename”) || die “Unable to read\n”;

while (<NAME>) {

print “$_”;

}

Don’t be scared!