introduction to perl programming: the minimum to know! bioinformatic and comparative genome analysis...
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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 TekaiaInstitut Pasteur
perl
A basic program
#!/bin/perl
# Program to print a message
print 'Hello world.'; # Print a message
Variables, Arrays
$val=9;
$val=“9”;
$val=“ABC transporter”;
• case sensitive: $val is different from $Val
Perl uses arithmetic operators:$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
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
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);
@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');
@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’ );
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
%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
File handling
#!/bin/perl
open(FILE,”GMG.pep”);
while <FILE>
{
print $_;
}
close (FILE);
a script (cat.pl) equivalent to the UNIX cat:
use: chmod a+x cat.pl ; cat.pl
split
#!/bin/perl
open(FILE,”GMG.pep”);
while <FILE>
{
@tab=split(/\s+/, $_);
print $tab[0];
}
close (FILE);
A very useful function in perl: splits up a string and places it into an array.
#!/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);
Control structures
foreachTo 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
}
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
}
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 $a false?
for
for (initialise; test; inc){
first_action; second_action; etc....
}
for ($i = 0; $i < 10; ++$i) # Start with $i = 1# Do it while $i < 10#Increment $i before repeating
{print "$i\n";
}
Conditionals
if ($a){
print "The string is not empty\n";}else{
print "The string is empty\n";}
#!/bin/perl
open(FILE,”GMG.pep”);
while <FILE>
{print $_ if ( m/>/ );}
close (FILE);
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
\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
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
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 casetr/A-Z/a-z/; #converts $_ to lower case