Perl Programming

Introduction to programming in Perl

WS 2006/07: Bioinformatics I

Introduction to programming in Perl Nicodème Paul [email protected]

http://www2.biozentrum.unibas.ch/personal/schwede/Teaching/BixI-WS0607/frame.htm

01-11-06

1

What is programming ? Introduction to programming in Perl

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Programming is breaking a task into small steps (divide and conquer). Sum : 15 + 25 + 11 ?

15 + 25 + 11 40

+ 11

51

Programs are written in a programming language such as : Fortran, Pascal, C, C++, java, Perl, Python, ….

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Program translator Introduction to programming in Perl

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Computer

Processor Program

Compiler or Interpreter

0101011

Memory

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What is Perl ? Introduction to programming in Perl

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Perl : Practical Extraction and Report Language by Larry Wall (1987) • Text-processing language • Glue language • Very high level language • perl is the language compiler/interpreter program

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Why do we use Perl? Introduction to programming in Perl

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• Simplicity • Rapid prototyping • Portability • Widely used in Bioinformatics

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A first example Introduction to programming in Perl

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#!/usr/bin/perl

# shebang line

# Pragmas use strict; use warnings;

# Restrict unsafe constructs # Provide helpful diagnostics

# Assign 15 to $number1 my $number1 = 15; # Assign 25 to $number2 my $number2 = 25; # Assign 11 to $number3 my $number3 = 11;

$number1 = $number1 + $number2; $number1 = $number1 + $number3; print “My result is : $number1\n”;

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# $number1 contains 40 # $number1 contains 51 # Print the result on the terminal

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Scalar Data Type Introduction to programming in Perl

• • • • • •

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$answer = 36; $pi = 3141659265 $avocados = 6.02e23; $language = “Perl”; $sign1 = “$language is nice”; $sign2 = ‘$language is nice’;

# an integer # a real number # scientific notation # a string # string with interpolation # string without interpolation

Scalar = singular variable $

S

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Scalar Binary Operators Introduction to programming in Perl

$u = 17

$v = 3

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$s = “Perl”

Name

Example

Result

Addition

$u + $v

17 + 3 = 20

Subtraction

$u - $v

17 – 3 = 14

Multiplication

$u * $v

17 * 3 = 51

Division

$u / $v

17 / 3 = 5.66666666667

Modulus

$u % $v

17 % 3 = 2

Exponentiation

$u ** $v

17 ** 3 = 4913

Concatenation

$s . $s

“Perl” . “Perl” = “PerlPerl”

Repetition

$s x n

“Perl” x 3 = “PerlPerlPerl”

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Scalar Unary Operators Introduction to programming in Perl

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Numbers

Strings

abs(expr)

uc(expr)

sqrt(expr)

lc(expr)

exit(expr)

chop(variable)

exp(expr)

chomp(variable)

int(expr)

reverse(expr)

log(expr)

length(expr)

¾ perldoc –f function_name 01-11-06

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Context Introduction to programming in Perl

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$u = “12” + 5; ¾17 $u = “12john” +5; ¾17 $u = “john12” + 5; ¾5

use strict; $u = “john12” + 5; ¾ Argument “john12” isn’t numeric in addition (+) at line 3 ¾5 $u = “12” + 5; ¾17 01-11-06

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Array data type Introduction to programming in Perl

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Values

Indices

0

35

1

12.4

2

“bye\n”

3

1.7e23

4

‘Hi’

$data[0] = 35; $data[1] = 12.4; $data[2] = “bye\n”; $data[3] = 1.7e23; $data[4] = ‘Hi’; @data = (35, 12.4, “bye\n”, 1.7e23, ‘Hi’)

Array = plural variable @

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a

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Array operators Introduction to programming in Perl

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@let = (“J”, “P”, “S”, “D”, “C”);

pop

$r=pop(@let)

$r=“C” @let=(“J”,“P”,“S”,“D”)

push

push(@let,“G”)

@let=(“J”,“P”,“S”,“D”,”C”,“G”)

shift

$r=shift(@let)

$r=“J” @let=(“P”,“S”,“D”,“C”)

unshift

unshift(@let,”G”)

@let=(“G”,“j”,“P”,“S”,“D”,“C”)

splice

@a=splice(@let,1,2)

@a=(“P”,”S”) @let=(“J”,”D”,”C”)

join

$r=join(‘:’,@let)

$r=“J:P:S:D:C”

scalar

$r=scalar(@let)

$r=5

reverse @a=reverse(@let) 01-11-06

@a=(“C”,”D”,”S”,”P”,”J”)

¾ perldoc –f function_name

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Search for a name Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; my @names = (“John”, “Peter”, “Simon”, “Dave”, “Chris”); my $offset = int(rand(scalar(@names))); # random index in [0, …, 4], int(2.55) = 2 if ($names[$offset] eq “Simon”) { # block start for the if statement print “Simon is found\n”; print “Success!\n”; } # block end for the if statement else { # block start for the else statement print “Simon is not found\n”; print “Failed!\n”; } # block end for the else statement

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Comparison operators Introduction to programming in Perl

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Comparison

Numeric

String

Return Value

Equal

==

eq

1 if $a is equal to $b , otherwise “”

Not equal

!=

ne

1 if $a is not equal to $b , otherwise “”

Less than

<

lt

1 if $a is less than $b , otherwise “”

Greater than

>

gt

1 if $a is greater than $b , otherwise “”

Less than or equal

<=

le

1 if $a is not greater than $b , otherwise “”

Greater than or equal

>=

ge

1 if $a is not less than $b , otherwise “”

Comparison

<=>

cmp

0 if $a and $b are equal, 1 if $a is greater, -1 if $b is greater

“” is the empty string

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What is true or false? Introduction to programming in Perl

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•

Any number is true except for 0.

•

Any string is true except for “” and “0”.

•

Anything else converted to a true value string or a true value number is true.

•

Anything that is not true is false.

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Logical operators Introduction to programming in Perl

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Example

Name

Result

$a && $b

AND

$a if $a is false, $b otherwise

$a || $b

OR

$a if $a is true, $b otherwise

! $a

NOT

True if $a is not true, false otherwise

$a and $b

AND

$a if $a is false, $b otherwise

$a or $b

OR

$a if $a is true, $b otherwise

not $a

NOT

True if $a is not true, false otherwise

$a xor $b

XOR

True if $a or $b is true, false if both are true

Pay attention to precedence rule : $xyz = $x || $y || $z

is not the same as

$xyz = $x or $y or $y

! Use parentheses !

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Conditional statements Introduction to programming in Perl

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• Simple Statement if (Expression); • Compound if (Expression) Block if (Expression) Block else Block if (Expression) Block elsif (Expression) Block else Block

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Search for a name Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; my @names = (“John”, “Peter”, “Simon”, “Dave”, “Chris”); my $offset = int(rand(scalar(@names))); my $count = 1; while($names[$offset] ne “Simon”) { # block start for the while statement $offset = int(rand(scalar(@names))); $count = $count + 1; } # block end for the while statement print “Simon is found after $count trials\n”;

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Check for a name Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; my @names = (“John”, “Peter”, “Simon”, “Dave”, “Chris”); for (my $i = 0; $i < scalar(@names); $i = $i + 1) { # block start for the for loop if ($names[$i] eq “Simon”) { print “Simon is found\n”; } } # end block for the for loop

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Check for a name Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; my @names = (“John”, “Peter”, “Simon”, “Dave”, “Chris”); for (my $i = 0; $i < scalar(@names); $i = $i + 1) { # block start for the for loop if ($names[$i] eq “Simon”) { print “Simon is found\n”; last; # jump outside of the loop } } # end block for the for loop

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Loop statements Introduction to programming in Perl

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Simple Statement while (Expression);

•

Compound while (Expression) Block for (Initialization; Expression; Incrementing) Block

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Hashes Introduction to programming in Perl

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Values

Keys

John

5

Peter

3

Simon

11

Dave

1

Chris

4 %names

$names{“John”} = 5; $names{“Peter”} = 3; $name{“Simon”} = 11 $names{“Dave”} = 1 $names{“Chris”} = 4

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%

Key/value

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Check for a name Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; my %names = (“John”, 5, “Peter”, 3, “Simon”, 11, “Dave”, 1, “Chris”, 4); my $key = “Simon”; if (exists $names{$key}) { exists return true if the key is in %names otherwise false print “$key is found, his value is : $names{$key}\n”; } else { print “$key is not found\n”; }

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Check for a name Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; my %names = ( “John” => 5, “Peter” => 3, “Simon” => 11, “Dave” => 0, “Chris” => 4 ); my $key = “Simon”; if (exists $names{$key}) { print “$key is found, his value is : $names{$key}\n”; } else { print “$key is not found\n”; } 01-11-06

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Hash operators Introduction to programming in Perl

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exists

exists $hash{$key}

Returns true if $key is in %hash, otherwise it returns false

delete

delete $hash{$key}

Deletes $key => $hash{$key} from %hash.

each

each %hash

Steps through a hash one key/value pair at a time

keys

keys %hash

Returns a list consisting of all the keys of %hash

values

Values %hash

Returns a list consisting of all the keys of %hash

¾ perldoc –f function_name 01-11-06

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Getting user input Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; my $line; print “Type something : “; while ($line = <STDIN>) { # STDIN : Standard Input if ($line eq “\n”) { print “That was just a blank line\n”; } else { print “Input : $line”; } print “Type something : “; }

¾ Ctr-C to exit 01-11-06

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Reading from a file Introduction to programming in Perl

WS 2006/07: Bioinformatics I

#!/usr/bin/perl use strict; use warnings; print “Enter the filename: “; my $filename = <STDIN>; # Read Standard Input for a # filename chomp($filename); # Remove the end of line character if (! (-e $filename)) { # Test whether the file exists print “File not found\n”; exit 1; }

Input file John Peter Simon Dave Chris

open(IN, $filename) || die “Could not open $filename\n”; my @names = ; # Store the content of the file in an array close(IN); print @names;

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Reading from a file Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; print “Enter the input file name : “; my $filename = <STDIN>; # Read Standard Input for a filename chomp($filename); # Remove the end of line character if (! (-e $filename)) { print “File not found\n”; exit 1; } my %names = (); my ($key, $value); open(IN, $filename) || die “Could not open $filename\n”; while ($line = ) { chomp($line); ($key, $values) = split(‘\t’, $line); $name{$key} = $value; } close(IN); $, = “ “; # It contains the separator for the print statement print %names, “\n”; 01-11-06

Input file : data.txt John Peter Simon Dave Chris

5 3 11 1 4

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Input and output functions Introduction to programming in Perl

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open

open FILEHANDLE, EXPR

open a file to referred using FILEHANDLE

close

Close FILEHANDLE

Close the file associated with FILEHANDLE

print

print [FILEHANDLE] LIST

Print each element of LIST to FILEHANDLE

¾ perldoc –f function_name

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Testing files Introduction to programming in Perl

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Example

Name

Result

-e $filename

Exists

True if file named in $a exists, otherwise false

-r $filename

Readable

True if file named in $a is readable, otherwise false

-w $filename

Writable

True if file named in $a is writable, otherwise false

-d $filename

Directory

True if file named in $a is a directory, otherwise false

-f $filename

File

True if file named in $a is a regular file, otherwise false

-T $filename

Text File

True if file named in $a is a text file, otherwise false

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Regular expressions Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; My $filename = “data.txt”; my $line; my %data = (); my $key;

Input file : data.txt

open(IN, $filename) || die “Could not open $filename\n”; while ($line = ) { chomp($line); if ($line =~ /^>/) { # check for ids using pattern matching $key = $line; } else { data{$key} = $line; } } close(IN); my @ids = keys %data; my @sequences = values %data; $, = “ “; print @ids, “\n”, @sequences, “\n”; 01-11-06

>id1 ATTGTC >id2 GGTCCT >id3 TATGAAA >id4 GTGTATA

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Regular expressions Introduction to programming in Perl

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EXPR =~ m/PATTERN/ m// Operator (Matching): searches the string in the scalar EXPR (or $_) for PATTERN; in scalar context the operator returns true (1) if successful, false (””) otherwise; in list context m// returns a list of substrings matched by any capturing parentheses in PATTERN; PATTERN undergoes double-quote interpolation. $line = “>id1” => $line =~ /^>/

VAR =~ s/PATTERN/REPLACEMENT/ s/// Operator (Substitution): searches the string in scalar variable VAR (or $_) for PATTERN and, if found, replaces the matched substring with the REPLACEMENT text; in scalar and list context s// returns the number of times it succeeded; both PATTERN and REPLACEMENT undergo double-quote interpolation. $line = “>id1” => $line =~ s/>//

VAR =~ tr/SEARCHLIST/REPLACEMENTLIST/ tr/// Operator (Transliteration): scans the string in scalar variable VAR (or $_) , character by character, and replaces each occurrence of a character found in SEARCHLIST with the corresponding character in REPLACEMENT list; in scalar and list context tr// returns the number of characters replaced or deleted; SEARCHLIST is NOT a regular expression and both SEARCHLIST and REPLACEMENT list do not undergo full double-quote interpolation (backslash sequences but no variable interpolation). $line = “id1” => $line =~ tr/a-z/A-Z/ 01-11-06

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Regular expressions Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings; my $filename = “data.txt”; my $line; my %data = (); my $key;

Input file : data.txt

open(IN, $filename) || die “Could not open $filename\n”; while ($line = ) { chomp($line); if ($line =~ /^>/) { #check for ids using pattern matching $line =~ s/>//; #substitute > by nothing in id $line =~ tr/a-z/A-Z/; #translate lower case to upper case $key = $line; } else { data{$key} = $line; } } close(IN); my @ids = keys %data; my @sequences = values %data; $, = “ “; print @ids, “\n”, @sequences, “\n”;

>id1 ATTGTC >id2 GGTCCT >id3 TATGAAA >id4 GTGTATA

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Regular expressions Introduction to programming in Perl

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Symbol

Meaning

\...

Used to escape metacharacters (including itself) or to make the next character a metacharacter (like \s, \w, \n)

...|... Alternation (match one or the other) (...)

Grouping (treat as a unit)

[...]

Character class (match one character from a set)

^

True at the beginning of string (or sometimes after any newline)

$

True at the end of the string (or sometimes before any newline)

.

Match any one character (except newline, normally)

$seq =~ /AAA$/

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Regular expressions Introduction to programming in Perl

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Quantifier

Meaning

*

Match 0 or more times (maximal)

+

Match 1 or more times (maximal)

?

Match 0 or 1 time (maximal)

{COUNT}

Match exactly COUNT times

{MIN,}

Match at least MIN times (maximal)

{MIN,MAX}

Match at least MIN times but not more than MAX times (maximal)

*?

Match 0 or more times (minimal)

+?

Match 1 or more times (minimal)

??

Match 0 or 1 time (minimal)

{MIN,}?

Match at least MIN times (minimal)

{MIN,MAX}?

Match at least MIN times but not more than MAX times (minimal)

$seq=“TATGAAA”

$seq =~ /.*AAA$/

$seq =~ /.*A{3}$/

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Regular expressions Introduction to programming in Perl

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Symbol

Meaning

Character Class

\d

Digit

[0-9]

\D

Nondigit

[^0-9]

\s

Whitespace

[ \t\n\r\f]

\S

Nonwhitespace

[^ \t\n\r\f]

\w

Word character

[a-zA-Z0-9_]

\W

Non-(word character)

[^a-zA-Z0-9_]

$id = “id2” 01-11-06

$id =~ /id\d+$/ 36

Subroutines or functions Introduction to programming in Perl

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#!/usr/bin/perl use strict; use warnings;

Input file : data1.txt

my $filename1 = “data1.txt”; my $filename2 = “data2.txt”; my %data1 = get_data($filename1); #subroutine call my %data2 = get_data($filename2); #subroutine call $, = “ “; print keys %data1, “\n”, values %data2, “\n”; print keys %data1, “\n”, values %data2, “\n”; sub get_data { my $filename = shift(@_); my $key; my %tmp = (); open(IN, $filename) || die “Could not open $filename\n”; while (my $line = ) { chomp($line); if ($line =~ /^>/) { $line =~ s/>//; $line =~ tr/a-z/A-Z/; $key = $line; } else { $tmp{$key} = $line; } } close(IN); return %tmp; }

>id1 ATTGTC >id2 GGTCCT >id3 TATGAAA >id4 GTGTATA

Input file : data2.txt >id5 ATAAAAA >id6 GGAATTT >id7 TATGATT >id8 GTGTAAT

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37

Packages Introduction to programming in Perl

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#!/usr/bin/perl

package MyTools;

use strict; use warnings; use MyTools;

sub get_data { my $filename = shift(@_); my $key; my %tmp = (); open(IN, $filename) || die “Could not open $filename\n”; while (my $line = ) { chomp($line); if ($line =~ /^>/) { $line =~ s/>//; $key = $line; } else { $tmp{$key} = $line; } } close(IN); return %tmp; } 1; # this should be your last line

my $filename1 = “data1.txt”; my $filename2 = “data2.txt”; my %data1 = MyTools::get_data($filename1); my %data2 = MyTools::get_data($filename2); $, = “ “; # set the print separator print keys %data1, “\n”, values %data1, “\n”; print keys %data2, “\n”, values %data2, “\n”;

Comprehensive Perl Archive Network (CPAN) http://www.cpan.org/ 01-11-06

38

References Introduction to programming in Perl

•

WS 2006/07: Bioinformatics I

Recommended Books – Beginner » “Learning Perl”, 4th Edition by Randal Schwartz, Tom Phoenix & Brian D Foy

» “Beginning Perl for Bioinformatics”, 1st Edition by James Tisdall

» Edition by Cynthia Gibas & PerJambeck » “Developing Bioinformatics Computer Skills”, 1st 01-11-06

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