1. Introduction to perl programming: the minimum to know! Bioinformatic and Comparative Genome Analysis Course HKU-Pasteur Research Centre - Hong Kong, China August 17 - August 29, 2009 Bioinformatic and Comparative Genome Analysis Course HKU-Pasteur Research Centre - Hong Kong, China August 17 - August 29, 2009 Fredj Tekaia Institut Pasteur tekaia@pasteur.fr

2. perl A basic program #!/bin/perl # Program to print a message print 'Hello world.';# Print a message

3. Variables, Arrays $val=9; $val=ABC transporter; case sensitive: $val is different from $Val

4. Perl uses arithmetic operators: $a = 1 + 2;# Add 1 and 2 and store in $a $a = 3 - 4; # Subtract 4 from 3 and store in $a $a = 5 * 6;# Multiply 5 and 6 $a = 7 / 8;# Divide 7 by 8 to give 0.875 $a = 9 ** 10;# Nine to the power of 10 $a = 5 % 2;# Remainder of 5 divided by 2 $a++;# Return $a and then increment it $a--;# Return $a and then decrement it for strings perl has among others: $a = $b. $c;# Concatenate $b and $c $a = $b x $c;# $b repeated $c times Operations and Assignment

5. To assign values perl includes $a = $b;# Assign $b to $a $a += $b;# Add $b to $a $a -= $b;# Subtract $b from $a $a.= $b;# Append $b onto $a

6. Array variables An array variable is a list of scalars (ie numbers and/or strings). they are prefixed by: @ @SEQNAME = (MG001", MG002", MG003"); $SEQNAME [2] (MG003) Attention: 0, 1, 2,.... @num = (0,1,2,3);

7. @L_CODONS = ('TTT','TTC','TTA','TTG', 'CTT','CTC','CTA','CTG', 'ATT','ATC','ATA','ATG', 'GTT','GTC','GTA','GTG', 'TCT','TCC','TCA','TCG', 'CCT','CCC','CCA','CCG', 'ACT','ACC','ACA','ACG', 'GCT','GCC','GCA','GCG', 'TAT','TAC','TAA','TAG', 'CAT','CAC','CAA','CAG', 'AAT','AAC','AAA','AAG', 'GAT','GAC','GAA','GAG', 'TGT','TGC','TGA','TGG', 'CGT','CGC','CGA','CGG', 'AGT','AGC','AGA','AGG', 'GGT','GGC','GGA','GGG');

8. @AA = ('A','R','N','D','C','Q','E','G','H','I','L','K','M','F','P','S','T','W','Y','V','B'); @mm = ( 'a','r','n','d','c','q','e','g','h','i','l','k','m','f','p','s','t','w','y','v','b );

9. Associative arrays : hash tables Ordinary list arrays allow us to access their element by number. The first element of array @AA is $AA[0]. The second element is $AA[1], and so on. But perl also allows us to create arrays which are accessed by string. These are called associative arrays. array itself is prefixed by a % sign

10. %ages = (Michael", 39, "Angie", 27, "Willy", "21 years", "The Queen Mother", 108); $ages{"Michael"};# Returns 39 $ages{"Angie"};# Returns 27 $ages{"Willy"};# Returns "21 years" $ages{"The Queen Mother"};# Returns 108

11. File handling #!/bin/perl open(FILE,GMG.pep); while { print $_; } close (FILE); a script (cat.pl) equivalent to the UNIX cat: use: chmod a+x cat.pl ; cat.pl

12. split #!/bin/perl open(FILE,GMG.pep); while { @tab=split(/ \s+/, $_); print $tab[0]; } close (FILE); A very useful function in perl: splits up a string and places it into an array.

13. #!/bin/perl open(FILE,GMG.pep); while { @tab=split(/ \s+/, $_, 2); $NOM{$tab[0]} = $tab[1]; print $NOM{$tab[0]} ; } close (FILE); @tab=split(/\s+/,$_,n);

14. Control structures foreach To go through each line of an array or other list-like structure (such as lines in a file) perl uses the foreach structure. This has the form foreach $nom (@SEQNAME)# Visit each item in turn # and call it $nom { print "$nom\n";# Print the item }

15. foreach $j ( 0.. 2)# Visit each value in turn # and call it $j { print "$SEQNAM [$j] \n";# Print the item } foreach $j ( 0.. $#AA)# Visit each value in turn # and call it $j { print "$AA [$j] \n";# Print the item }

16. Testing Here are some tests on numbers and strings. $a == $b# Is $a numerically equal to $b? #Beware: Don't use the = operator. $a != $b# Is $a numerically unequal to $b? $a eq $b# Is $a string-equal to $b? $a ne $b# Is $a string-unequal to $b? You can also use logical and, or and not: ($a && $b)# Is $a and $b true? ($a || $b)# Is either $a or $b true? !($a)# is $a false?

17. for for (initialise; test; inc) { first_action; second_action; etc.... } for ($i = 0; $i < 10; ++$i)# Start with $i = 1 # Do it while $i < 10 # Increment $i before repeating { print "$i\n"; }

18. Conditionals if ($a) { print "The string is not empty\n"; } else { print "The string is empty\n"; } #!/bin/perl open(FILE,GMG.pep); while { print $_ if ( m/>/ ); } close (FILE);

19. String matching $a eq $b# Is $a string-equal to $b? $a ne $b# Is $a string-unequal to $b? Here are some special RE characters and their meaning.# Any single character except a newline ^# The beginning of the line or string $# The end of the line or string *# Zero or more of the last character +# One or more of the last character ?# Zero or one of the last character

20. \n# A newline \t# A tab \w# Any alphanumeric (word) character. # The same as [a-zA-Z0-9_] \W# Any non-word character. # The same as [^a-zA-Z0-9_] \d# Any digit. The same as [0-9] \D# Any non-digit. The same as [^0-9] \s# Any whitespace character: space, # tab, newline, etc \S# Any non-whitespace character \b# A word boundary, outside [] only \B# No word boundary Some more special characters

21. Characters like $, |, [, ), \, / and so on are peculiar cases in regular expressions. If you want to match for one of those then you have to preceed it by a backslash (\). So: \|# Vertical bar \[# An open square bracket \)# A closing parenthesis \*# An asterisk \^# A carat symbol \/# A slash \\# A backslash

22. Substitution and translation s/london/London/ $sentence =~ s/london/London/ global substitution; i option (for "ignore case"). s/london/London/gi Translation $sentence =~ tr/abc/edf/ tr/a-z/A-Z/; #converts $_ to upper case tr/A-Z/a-z/; #converts $_ to lower case

23. -given a nucleotide sequence: base composition -given a protein sequence: amino-acid composition; -given a nucleic databse (in fasta format): base composition -given a protein database (in fasta format): amino-acid composition Simple scripts

24. -sequence size (base or amino-acids) -extract a portion of a sequence: (pos start; pos end) -extract a sequence by name (from a database of sequences) -gene sequence: codon count; given allxxseqnew file: -script to compute frequencies of multiple matches; see splitfasta.pl; splitdnafasta.pl

25. given allxxseqnew file: -script to compute frequencies of multiple matches; Exercices de manipulation des données : - home-directory, mkdir, cd, pathway, pwd, find ; - notation : DB.pep, DB.dna, seq.dna, seq.prt ; - utiliser « tab » comme séparateur ; - utilisation de sed et de grep ; - le format fasta des séquences ; - compter le nombre des séquences dans une base de séquences au format fasta ; (grep « > » DB.pep wc –l ) - changer un caractère par un autre : -extraire les séquences dune base (fichier au format fasta) (splitfasta.pl, splitdnafasta.pl); -extraire 1 partie dune séquence (la séquence est au format fasta); -fréquence des aa dune séquence protéique ; -fréquence des bases dune séquence nucléotidique ; -taille dune séquence ; -tailles des séquence dune base ; -fréquence des codons dune séquence codante ; -Codons volatilité :. correspondance codons/amino-acids ;