one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation &...

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Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier

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Page 1: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Introduction to Perl programmation & one line of Perl program

BOCS StéphanieDROC GaëtanARGOUT Xavier

Page 2: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Introduction

❑ What is Perl ?▪ PERL (Practical Extraction and Report Language) created in 1986 by Larry Wall▪ Programming language▪ Interpreted langage (no compilation)

❑ Why Perl ?▪ Portability (Unix, Windows, Mac) ▪ Simplicity ▪ Object ▪ In biology, many libraries have been created (BioPerl)

❑ Which uses ?▪ Manipulate files (conversion of file format) and text (search of regular expressions) ▪ Handling processes (system call) and run programs (workflow)

Page 3: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Scalar variable: $

❑ Single value (number or string)❑ Declaring a variable ‘my’

my $name; # ‘#’ comment ‘;’ indicates end of an instruction❑ Assigning a value ‘=‘

my $number = 4;

my $dna = "ATCGATAGACAT";

❑ Standard input ‘<>’print " Please type a number : \n";

my $number = <STDIN>;

print " Your number is $number\n";

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Operators, functions & numerical context

❑ Classical operators are available: +, -, /, *, % ❑ Shortcuts +=, -=, *=, /=

$x += 3; is equivalent to $x = $x + 3; ❑ Auto-incrementers et Auto-decrementers

$a++; is equivalent to $a = $a + 1;$a--;

❑ Some mathematical functions :▪ abs($x); returns absolute value of $x. ▪ sqrt($x); returns the square root of $x. ▪ int($x/$y); is the quotient of the integer division of $x by $y.▪ sin($x); cos($x); return the sine and the cosine of $x. ▪ exp($x); log($x); return e power $x and logarithm in base e of $x.

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Operators, functions & string context

❑ Concatenation$c = 'ce' . 'rise'; (=> $c becomes 'cerise')

$c .= 's'; (=> $c becomes 'cerises') ❑ Replica

$b = 'a' x 5; => 'aaaaa'$b = 'jacqu' . 'adi' x 3; => 'jacquadiadiadi'

❑ Some string functions ▪ length($x); returns string length $x▪ chop($x); remove the last character of the string $x ▪ chomp($x); remove the last character of the string $x if it is a newline (\n)▪ reverse($x); returns a string composed of $X characters but in the reverse order. ▪ substr($x,offset,length); return the substring from position ‘offset’ and length

‘length.▪ index($string,$substring,$position); returns the position of the first occurrence

of $substring in $string.▪ rindex($string,$substring,$position); same as index but starting from the end of

the string

Page 6: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Test & Boolean operators

❑ Test operators

❑ Boolean operators▪ (expr1 && expr2) is true if expr1 AND expr2 are true

▪ (expr1 || expr2) is true if expr1 OR expr2 are true

▪ (!expr) is true if expr is false.

context numerical string

equality == eq

difference != ne

Lower than < lt

Greater than > gt

Lower or equal <= le

Greater or equal >= ge

comparison <=> cmp

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Control structures (condition)

▪ Defined by the instruction: IF, ELSIF and ELSE if( condition1 ) { instructions1; } elsif( condition2 ) { instructions2; } else { instructions3; }

▪ Ex: if( $x == $y )

{

print "\$x et \$y sont égaux\n";

}

else

{

print "\$x et \$y sont différents\n";

}

▪

Page 8: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Control structures (loop)

▪ Instructions: FOR and WHILE for( initialisation; condition; incrément ) { instructions; }

while( condition ) { instructions; }

▪ Ex: for( my $i=0; $i<=20; $i+=2 ) { print "$i\n"; }

my $i = 0; while( $i <= 20 ) { print "$i\n"; $i+=2; }

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Regular expressions: set and quantifier

▪ Syntax:.: Any character[]: Any character in the brackets: e.g. [AFTR] either A or F or T or R\d : an interger\w : an alphanumeric character\s : a space* : 0 or more times+ : 1 or more times? : 0 or 1{n} : n times

▪ Defined variable $1, $2, etc.: correspond to substrings that match regular expression between parentheses▪ Ex : my $v = "za aa et tfe"; if( $v =~ /(a+) et ([a-z])/ ) { print "$1\n"; # 'aa' print "$2\n"; # 't' }

Page 10: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

$ perl -h

Usage: perl [switches] [--] [programfile] [arguments]

-0[octal] specify record separator (\0, if no argument)

-a autosplit mode with -n or -p (splits $_ into @F)

-C[number/list] enables the listed Unicode features

-c check syntax only (runs BEGIN and CHECK blocks)

-d[:debugger] run program under debugger

-D[number/list] set debugging flags (argument is a bit mask or alphabets)

-e program one line of program (several -e's allowed, omit programfile)

-f don't do $sitelib/sitecustomize.pl at startup

-F/pattern/ split() pattern for -a switch (//'s are optional)

-i[extension] edit <> files in place (makes backup if extension supplied)

-Idirectory specify @INC/#include directory (several -I's allowed)

-l[octal] enable line ending processing, specifies line terminator

-[mM][-]module execute "use/no module..." before executing program

-n assume "while (<>) { ... }" loop around program

Page 11: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Exercice1: one line of Perl program

Convert a file in fasta format (2 lines per sequence) to a excel file (1 line per sequence)

Read the /usr/local/bioinfo/training/Perl/exercice1.txt▪ od –c▪ dos2unix▪ perl –ne▪ Tail▪ echo & cat

Special characters▪ \n: new line

▪ \r: carriage return

▪ \t: tabulation

▪ \f: new page

▪ \e: escape

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Exercice2: substitution

▪ Functionalities : correspondence et substitution

▪ Syntax:m/pattern/: correspondences/pattern/string/: substitution

▪ Syntax example: if( $v =~ m/motiv/ )

{

instructions

}

▪ Read the /usr/local/bioinfo/training/Perl/exercice2.txt

Page 13: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

❑ Create a program: hello.pl

#!/usr/bin/perl

print "Hello word!!!\n";

First steps to create a program

ShebangSpecifies to the operating system where is the Perl executable.Always at the first line of the file.

Predefined function that will display on the screen the string "Hello world"

New line operator

The character ‘;’ indicates the end of a instruction in the perl file (like the end of a sentence in a text)

Page 14: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

❑ Create a program: hello_yourname.pl#!/usr/bin/perl

print "Hello word!!!\n";

❑ Make the program executablechmod +x hello.pl

./hello_yourname.pl

❑ Give parameters to the programm#!/usr/bin/perl

my $name = shift;

print "Hello $name!!!\n";

❑ Run the program$ ./hello_yourname.pl Toto

Exercice3: Create a program hello.pl

Page 15: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

List and array: @

▪ A list is a suite of scalar values▪ An array is variable which can contain a list▪ Declaration

my @tab;

▪ A list is represented by the values that it should contain enclosed in parenthesis

(2,‘age’,$variable)

▪ To assign a list to an arraymy @tab=(3,$chaine,4);

▪ Access to a value in the table : index conceptmy @tab=(3,$chaine,4);

$tab[0] 3 $tab[1] valeur de $chaine $tab[2] 4

index 0 index 1 index 2

Page 16: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Functions to manipulate tables

my @t = (1, 2, 3, 4);

▪ Unshift: uses an array and a list and add the list to the top of the table

ex: unshift(@t, 5, 6); -> @t is (5,6,1,2,3,4)

▪ shift: removes the first element of the tab and returns it

ex: $v = shift(@t); -> $v is 1 and @t is (2,3,4)

▪ push: uses an array and a list and add the list to the end of the table

ex: push(@t, 5, 6); -> @t is (1,2,3,4,5,6)

▪ Pop: removes the last element of the tab and returns it

Ex: $v = pop(@t); -> $v is 4 and @t is (1,2,3)

▪ Reverse: use an array and returns a reversed list without modifying the tab

Ex: @s = reverse(@t); -> @s is (4,3,2,1) and @t is not modified

Page 17: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Hash: %

▪ A hash is a data type to associate a value with a key. E.g. we will be able to associate phone numbers to person:

Paul: 01.23.45.67.89

Virginie: 06.06.06.06.06

Pierre: 06.28.33.55.66

▪ Déclaration :my %phone_hash ;

▪ Pour assigner des valeurs à une table de hachage :my %phone_hash = ( "Paul" => "01.23.45.67.89",

"Virginie" => "06.06.06.06.06",

"Pierre" => "06.28.33.55.66" );

▪ Accéder à un élément$phone_hash{"Paul"} is 01.23.45.67.89

Page 18: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Exercice4: Print hash structure: Data::Dumper

$ more printhash_yourname.pl #!/usr/bin/perl -wuse strict;use Data::Dumper;

my %hash = ("pcr" => {n1 => "10", n2 => "3"}, "alex" => {n1 => "03", n2 => "6"}, "zorro" => {n1 => "5", n2 => "4"});

print Dumper(\%hash);

$ ./printhash_stefi.pl $VAR1 = { 'zorro' => { 'n2' => '4', 'n1' => '5' }, 'pcr' => { 'n2' => ‘3', 'n1' => ’10' }, 'alex' => { 'n2' => '6', 'n1' => '03' } };

Give a reference to the Dumper function of the Data::Dumper moduleTo know more see links in comment

Page 19: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Exercice5: multiple Sort

Specify the column number$ sort -k 2 -n sort.txtpir 01 3zorro 01 20alex 03 6pcr 03 7par 04 5zero 5 4pur 10 3

Reverse$ sort -k 2 -n -r sort.txtpur 10 3zero 5 4par 04 5pcr 03 7alex 03 6zorro 01 20pir 01 3

$ more sort.txt pur 10 3alex 03 6zero 5 4par 04 5pcr 03 7pir 01 3zorro 01 20

$ sort sort.txtalex 03 6par 04 5pcr 03 7pir 01 3pur 10 3zero 5 4zorro 01 20

Sort on several fields$ sort -k2n -k1r sort.txtzorro 01 20pir 01 3pcr 03 7alex 03 6par 04 5zero 5 4pur 10 3

Page 20: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Exercice6: multiple Sort with hash

sort by keyalex 03 6par 04 5pcr 03 7pir 01 3pur 10 3zero 5 4zorro 01 20

$ tail sorthash_stefi.pl…print "\nsort by key\n";foreach my $key (sort (keys(%hash))) { print join("\t",$key,$hash{$key}->{n1}, $hash{$key}->{n2}),"\n";}

print "\nsort by value\n";foreach my $key(sort {$hash{$a}->{n1} <=> $hash{$b}->{n1} || $hash{$b}->{n2} <=> $hash{$a}->{n2}} keys(%hash)) { print join("\t",$key,$hash{$key}->{n1}, $hash{$key}->{n2}),"\n";}Returns a list consisting of all the keys of the named hash, or the indices of an array (In scalar context, returns the number of keys or indices).

sort by valuezorro 01 20pir 01 3pcr 03 7alex 03 6par 04 5zero 5 4pur 10 3

Page 21: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Manipulate files

▪ Operators :

open : open filewhile (<>) : browse fileclose : close file▪ Syntax ex: open F, "data.txt";

while (<F>)

{

instructions;

}

close F;

▪ You can open a file in read or write modeopen F, "data.txt"; : readopen F, ">data.txt"; : overwriteopen F, ">>data.txt”; : write by adding at the end of the file

Page 22: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Exercice7: read a file

#!/usr/bin/perl

my $fichier = "/home/sidibebocs/work/training_20140527/perl/name.txt";

open(F, "<$fichier”) or die "ce fichier n'existe pas\n”;

while (<F>)

{

chomp;

my $ligne=$_;

if ($ligne eq "Xavier")

{

print "$ligne Diplome : Master\n";

}

elsif ($ligne eq ("Stephanie" || "Manuel"))

{

print "$ligne Diplome : These\n";

}

else

{

print "$ligne Diplome : Inconnu\n";

}

}

Name.txtManuelXavierEstebanStephanieJean Pierre

Page 23: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Exercice8: write an output file

$ multiple2oneline.pl#!/usr/bin/perluse strict;

my $file = shift;my $file_out = $file . ".oneline";open(OUT,">$file_out");open(GENE,$file);

my %hash;

while(<GENE>){ chomp; my ($gene, $GO) = (split(/\t/,$_));

push @{$hash{$gene}},$GO;}close GENE;

foreach my $gene (keys %hash) {print OUT join("\t", $gene, @{$hash{$gene}}), "\n";

}close OUT;

$ ./multiple2oneline.pl prot2go_test.txt$ wc -l prot2go_test.txt* 1000 prot2go_test.txt 331 prot2go_test.txt.oneline

$ more prot2go_test.txtGSMUA_Achr10T03460_001 GO:0005525GSMUA_Achr10T03460_001 GO:0005622GSMUA_Achr10T03460_001 GO:0007264GSMUA_Achr10T03460_001 GO:0015031GSMUA_Achr10T03520_001 GO:0005524

$ more prot2go_test.txt.onelineGSMUA_Achr10T03460_001 GO:0005525 GO:0005622 GO:0007264 GO:0015031

Page 24: one line of Perl program Introduction to Perl programmation · Introduction to Perl programmation & one line of Perl program BOCS Stéphanie DROC Gaëtan ARGOUT Xavier. Introduction

Good programming practices

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