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Perl: basic programming examples
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Simple examples of Perl code.

<small>Parts of this code have been originally contributed by Sohrab Shah, Sanja Rogic, Wil Hsiao and others (let me know if you happen to read this and should be listed here) and these parts were taken from the [http://www.bioinformatics.ca Canadian Bioinformatics Workshop] bioinformatics course, where it has been made available through a [http://creativecommons.org/licenses/by-sa/2.5/ Creative Commons] license.</small>


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&nbsp;
==Contents==



==Exercise 1 - First print statement==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 print "My first Perl program\n"; <span style="color:#888888">#also try this with single quotes</span>
 print "First line\nsecond line and there is a tab\there\n";
 
 exit();

Notes:
# I '''always''' <tt>use strict;</tt> and <tt>use warnings;</tt>, even on the shortest programs. Mighty warts from tiny programs grow.
# I '''always''' end a program with <tt>exit();</tt> even though it is not necessary. Why? It immediately tells me where the program ends and that I have copied it completely from wherever I got it.

==Exercise 2 - Numerical variables and operators==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#assign values to variables $x and $y and print them out</span>
 my $x = 4;
 my $y = 5.7;
 print "x is $x and y is $y\n";
 
 <span style="color:#888888">#example of arithmetic expression</span>
 my $z = $x + $y**2;
 $x++;
 print "x is $x and z is $z\n"; 
 
 <span style="color:#888888">#evaluating arithmetic expression within print command</span>
 print "add 3 to $z: $z + 3\n"; <span style="color:#888888">#did it work?</span>
 print "add 3 to $z:", $z + 3,"\n";
 
 exit();

Notes:
# within "strings", variables are '''interpolated''', but not '''evaluated'''!
# however, within 'strings', variables are neither interpolated nor evaluated.
 
==Exercise 3 - String variables and operators==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#TASK: Concatenate two given sequences, 
 #find the length of the new sequence and
 #print out the second codon of the sequence</span>
 
 <span style="color:#888888">#assign strings to variables</span>
 my $DNA = "GATTACACAT";
 my $polyA = "AAAA";
 
 <span style="color:#888888">#concatenate two strings</span>
 my $modifiedDNA = $DNA . $polyA;
 
 <span style="color:#888888">#calculate the length of $modifiedDNA and</span>
 <span style="color:#888888">#print out the value of the variable and its length</span>
 my $DNAlength = length($modifiedDNA);
 print "Modified DNA: $modifiedDNA has length $DNAlength\n";
 
 <span style="color:#888888">#extract the second codon in $modifiedDNA</span>
 my $codon = substr($modifiedDNA,3,3);
 print "Second codon is $codon\n";
 
 exit();

==Exercise 4 - working with user input==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#TASK: Ask the user for her name and age and
 #calculate her age in days</span>
 
 <span style="color:#888888">#get a string from the keyboard</span>
 print "Please enter your name\n";
 my $name = <STDIN>;
 chomp($name); <span style="color:#888888">#getting rid of the new line character</span>
 
 <span style="color:#888888">#prompt the user for his/her age</span>
 <span style="color:#888888">#get a number from the keyboard</span>
 print "$name please enter your age\n";
 my $age = <STDIN>;
 chomp($age);
 
 <span style="color:#888888">#calculate age in days</span>
 my $age_in_days = $age*365;
 print "You are approximately $age_in_days days old\n";
 
 exit();

==Exercise 5 - Arrays==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#initialize an array </span>
 my @bases = ("A","C","G","T");
 
 <span style="color:#888888">#print two elements of the array</span>
 print $bases[0],$bases[2],"\n";
 
 <span style="color:#888888">#print the whole array</span>
 print @bases,"\n"; <span style="color:#888888">#try with double quotes</span>
 
 <span style="color:#888888">#print the number of elements in the array</span>
 print scalar(@bases),"\n";
 
 exit();

==Exercise 6 - While and if statements==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#TASK: Count the frequency of base G in a given DNA sequence</span>
 
 my $DNA = "GATTACACAT";
 
 <span style="color:#888888">#initialize $countG and $currentPos</span>
 my $countG = 0;
 my $currentPos = 0;
 my $base; 
 
 <span style="color:#888888">#calculate the length of $DNA</span>
 my $DNAlength = length($DNA);
 
 <span style="color:#888888">#for each letter in the sequence check if it is the base G</span>
 <span style="color:#888888">#if 'yes' increment $countG</span>
 while($currentPos < $DNAlength){
 	$base = substr($DNA,$currentPos,1);
 	if($base eq "G"){ 
 		$countG++;
 	}
 	$currentPos++;
 } <span style="color:#888888">#end of while loop</span>
 
 <span style="color:#888888">#print out the number of Gs</span>
 print "There are $countG G bases\n";
 
 exit();

==Exercise 7 - For and foreach loops==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 my @array;
 
 <span style="color:#888888">#initialize a 20-element array with numbers 0,...19</span>
 for (my $i=0;$i<20;$i++){
     $array[$i] = $i;
 }
 
  <span style="color:#888888">#print elements one-by-one using foreach</span>
 my $element;
  foreach $element (@array){
     print "$element\n";
 }
 
 exit();

Notes:

# a more Perl-ish way to write the first <tt>for</tt> loop would be the following ''(although personally I prefer the first version, often called C-style, as being more explicit).''

 my $i;
 for $i (0..19){
     $array[$i] = $i;
 }

==Exercise 8 - Regular expressions==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#TASK: For a given DNA sequence find its RNA transcript,
 #find its reverse complement and check if
 #the reverse complement contains a start codon</span>
 
 my $DNA = "GATTACACAT";
 
 <span style="color:#888888">#transcribe DNA to RNA - T changes to U</span>
 my $RNA = $DNA;
 $RNA =~ s/T/U/g;
 print "RNA sequence is $RNA\n";
 
 <span style="color:#888888">#find the reverse complement of $DNA using substitution operator
 #first - reverse the sequence</span>
 my $rcDNA = reverse($DNA);
 
 $rcDNA =~ s/T/A/g;
 $rcDNA =~ s/A/T/g;
 $rcDNA =~ s/G/C/g;
 $rcDNA =~ s/C/G/g;
 
 print "Reverse complement of $DNA is $rcDNA\n"; <span style="color:#888888">#did it work?</span>
 
 <span style="color:#888888">#find the reverse complement of $DNA using translation operator</span>
 
 <span style="color:#888888">#first - reverse the sequence</span>
 $rcDNA = reverse($DNA);
 $rcDNA =~ tr/ACGT/TGCA/;
 print "Reverse complement of $DNA is $rcDNA\n";
 
 <span style="color:#888888">#look for a start codon in te reverse sequence</span>
 if($rcDNA =~ /ATG/){
     print "Start codon found\n";
 }
 else{
     print "Start codon not found\n";
 }
 
 exit();

==Exercise 9 - Subroutines==

 #!/usr/bin/perl
 use strict;
 use warnings;
  
 <span style="color:#888888">#TASK: Make a subroutine that calculates the reverse
 #complement of a DNA sequence and call it from the main program</span>
 
 <span style="color:#888888">#body of the main program with the function call</span>
 my $DNA = "GATTACACAT";
 my $rcDNA = revcomp($DNA); 
 print "$rcDNA\n";
 
 exit();
 
 <span style="color:#888888">#definition of the function for reverse complement</span>
 sub revcomp{
     my($DNAin) = @_;
     my($DNAout) = reverse($DNAin);
     $DNAout =~ tr/ACGT/TGCA/;
     return $DNAout;
 }

Notes;
# Parameters are passed into a subroutine via the "anonymous array" <tt>'''@_'''</tt>. Accordingly, parameters must be assigned in a so called '''list context''' - note the parentheses around <tt>$DNAin</tt>! If you would omit the parenetheses,  <tt>$DNAin</tt> would be asigned in '''scalar context''', i.e. it would be assigned the length of the array, which is 1, one string element. This is a very common newcomer's mistake.

==Exercise 10 - Input and output files==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#TASK: Read DNA sequences from ‘DNAseq’ input file – 
 #there is one sequence per line
 #For each sequence find the reverse complement and 
 #print it to ‘DNAseqRC’ output file</span>
 
 
 <span style="color:#888888">#open input and output files</span>
 open(IN,"DNAseq");
 open(OUT,">DNAseqRC");
 
 <span style="color:#888888">#read the input file line-by-line
 #for each line find the reverse complement
 #print it in the output file</span>
 my $rcDNA;
 while(<IN>){
     chomp;
     $rcDNA = revcomp($_);
     print OUT "$rcDNA\n";
 }
 
 <span style="color:#888888">#close input and output files</span>
 close(IN);
 close(OUT);
 
 exit();
 
 <span style="color:#888888">#definition of the function for reverse complement</span>
 sub revcomp{
     my($DNAin) = @_;
     my($DNAout) = reverse($DNAin);
     $DNAout =~ tr/ACGT/TGCA/;
     return $DNAout;
 }

==Exercise 11 - System calls==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#TASK: Print a list of all Perl programs you wrote today.
 #These files can be found in your current directory and 
 #they end with the file extension ‘.pl’</span>
 
 print "List of programs I wrote today:\n";
 
 <span style="color:#888888">#system call for 'ls' function - the result goes into a string</span>
 my $listing = `ls`;  <span style="color:#888888">#these are back quotes</span>
 
 <span style="color:#888888">#split the string to get individual files</span>
 my @files = split(/\n/,$listing);
 
 <span style="color:#888888">#use foreach to step through the array
 #if a file contains the string '.pl' print it out</span>
 my $file; 
 foreach $file (@files){
     if($file =~ /\.pl$/){ <span style="color:#888888">#regular expression: the '.' is escaped "\."</span>
         print "$file\n";
     }
 }
 
 exit();

==Exercise 12 - Putting it all together==

 #!/usr/bin/perl
 use strict;
 use warnings;
 
 <span style="color:#888888">#TASK: Find the reverse complement of a gene, its GC content 
 #and the GC content of its reverse complement.
 #The gene is stored in a DNA.fasta file.</span>
 
 <span style="color:#888888">#body of the main program</span>
 
 <span style="color:#888888">#open input file</span>
 open(IN,"DNAfasta");
 
 <span style="color:#888888">#get a gene name</span>
 my $name = <IN>;
 chomp($name);
 
 #concatenate all lines from fasta file in one string</span>
 my $DNA = "";
 while(<IN>){ <span style="color:#888888">#input goes into $_</span>
     chomp;
     $DNA = $DNA . $_;
 }
 close(IN);
 
 <span style="color:#888888">#call functions to get the reverse complement and GC content</span>
 my $DNA_gc = gc_content($DNA);
 my $DNArc = revcomp($DNA);
 my $DNArc_gc = gc_content($DNArc);
 
 <span style="color:#888888">#print out the results</span>
 print "$name has GC content: $DNA_gc\n";
 print "reverse complement of $name has GC content: $DNArc_gc\n";
 
 exit();
 
 <span style="color:#888888"> #definition of the function for reverse complement</span>
 sub revcomp{
     my($DNAin) = @_;
     my $DNAout = reverse($DNAin);
     $DNAout =~ tr/ACGT/TGCA/;
     return ($DNAout);
 }
 
 <span style="color:#888888">#definition of GC content function</span>
 sub gc_content{
     my($DNAin) = @_;
     my $count = 0;	
     my $DNAlength = length($DNAin);
 
     <span style="color:#888888">#explode DNA string into an array</span>
     my @bases = split(//,$DNA);
 
     <span style="color:#888888">#step through the array and count the occurrences of G and C</span>
     for (my $i=0;$i<$DNAlength;$i++){
         if ($bases[$i] =~ /[GC]/){
             $count++;
         }
     }
     <span style="color:#888888">#return percentage of GC bases</span>
     return ($count/$DNAlength);
 }




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==Exercises==
<section begin=exercises />
<section end=exercises />


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==Notes==
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==Further reading and resources==
<!-- {{#pmid:21627854}} -->
<!-- {{WWW|WWW_UniProt}} -->
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->


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[[Category:Applied_Bioinformatics]]
[[Category:Perl]]
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