1. Introduction to perl programming: the minimum to know for practice!
Fredj Tekaia
Bioinformatics and Genome Analyses
Institut Pasteur Tunis, Tunisia. September 18 – December 15, 2017

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

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

4. Operations and Assignment
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 by 1
$a--; # Return $a and then decrement it by 1
for strings perl has among others:
$a = $b . $c; # Concatenate $b and $c
$a = $b x $c; # $b repeated $c times

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

7. Array variables @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. Array variables
@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 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.
The array itself is prefixed by a % sign

10. Associative arrays : hash tables
%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 a script (cat.pl) equivalent to the UNIX cat:
#!/usr/bin/perl
open(FILE,”GMG.pep”);
while <FILE> {
print $_; }
close (FILE);
use: chmod a+x cat.pl ; cat.pl

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

13. split #!/usr/bin/perl open(FILE,”GMG.pep”); while <FILE> {
@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 # Visit each item in turn
# and call it $nom {
print "$nom\n"; # Print the item }

15. Control structures 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";
#!/usr/bin/perl
open(FILE,”GMG.pep”);
while <FILE> {
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. Some more special characters
\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

21. Some more special characters
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. Practical session

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

25. Exercises: Simple scripts
-sequence size (bases 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

26. Exercises: Simple scripts
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 d’une base (fichier au format fasta) (splitfasta.pl, splitdnafasta.pl);
- extraire 1 partie d’une séquence (la séquence est au format fasta);
- fréquence des aa d’une séquence protéique ;
- fréquence des bases d’une séquence nucléotidique ;
- taille d’une séquence ;
- tailles des séquence d’une base ;
- fréquence des codons d’une séquence codante ;
- Codons volatilité :
. correspondance codons/amino-acids ;

27. Thank You