Perl IX: References Problem Set
 
Pre Questions:
 
P1. Create an array, retrieve the reference(address), print the reference(address).
    my @array = ('a' , 123, 'book' , 'end');
P2. Use the reference to print out the 2nd and 3rd elements.
P3. Create a hash, retrieve the reference (address), print the reference.
P4. Use the reference to print out a single key/value pair.
 
1. Modify your FASTA parser to create a hash of genes and store
    a. The sequenceID as a hash key (geneName)
    b. The sequence description as a inner key to geneName.
    c. The sequence as a inner key to the same key (geneName).
    d. The sequence length as a inner key to the same key (geneName).
    Hint: This is now a hash of hashes. The value of gene is really an anonymous hash.
 
$VAR1 = {
          'gene1' => { 
                        'seq' => "ATTC",
                        'desc' => 'the is a great seq',
                        'len' => 4,
           },
 
           'gene2' => { 
                        'seq' => "TTTT",
                        'desc' => 'the is a better seq',
                        'len' => 4,
 
            },
    };
 
 
2. Use Data::Dumper and its function Dumper to print out the hash to the screen (STDOUT).
 
3. Print out each gene and its information in a tab-delimited file (FILEHANDLE).
	a. Using a foreach loop, iterate through each key (sequenceID).
	b. Use key to iterate thru each inner key (seq desc, seq, length) and retrieve the values.
	c. print out all data delimited by tabs (\t).
		ex: seq1\tmy favorite gene\tATGCTGGGG\t9\n" 
	d. What about the header line ("Name\tDesc\tSeq\tlen\n")? Where do you need to print this so that it appears first and only once in your output.
 
 
4. Calculate and store the count of each nucleotide for each seq.
 	**** hint: $genes{$seqName}{'nt_count'}{$nt}=$count;
	**** hint: %gene is now a hash of hashes of hashes.
	a. Nucleotide count {'nt_count'} will be another value of the gene key. It is not a variable, it is a string. $genes{$seqName}{'nt_count'}
 
$VAR1 = {
          'gene1' => { 
                        'seq' => "ATTC",
                        'len' => 4,
                        'desc' => 'the is a great seq',
                        'nt_count' => { 
                            'a' => '1',
                            't' => '2'
                            'C' => '1'
                          },
           },
 
           'gene2' => { 
                        'seq' => "TTTT",
                        'len' => 4,
                        'desc' => 'the is a better seq',
                        'nt_count' => { 
                            't' => '4',
                          },
 
 
            },
    };
 
 
5. Calculate and add %GC content for each sequence to the hash for each gene as an additional value to the gene name key.
	a. Create a GC_content subroutine. 
 	b. Call the subroutine on each sequence 
	   my $GC = GC_content($seq);
	c. Use your already stored seq length and 'G' and 'C' total counts to calculate GC content
	d. Store the calculated %GC content as an additional value to gene key.
	e. use Data::Dumper to visualize your hash.
 
6. Print out only high %GC content sequences to a file called highGC.fasta in FASTA format.
	a. Create a subroutine called GC_filter.
	b. GC_filter takes the hash of genes and a minimum %GC cutoff. 
	c. GC_filter returns the number of sequences that met your %GC cutoff criteria or have a higher GC%.
	d. GC_filter also returns an array of arrays made up of gene names and sequences ([geneName,seq],[geneName,seq],[geneName,seq]).
	e. Example usage:  
	   my ($count, $array_of_arrays) = GC_filter (\%genes , 55);
 
$VAR1 = {
          'gene10' => { 
                        'seq' => "GCAT",
                        'len' => 4,
                        'desc' => 'the is a super seq',
                        'nt_count' => { 
                            'a' => '1',
                            't' => '1'
                            'C' => '1'
                            'G' => '1'
                          },
                         'GC'   => '50',
           },
}
 
 
7. Print out each gene and ALL of its information in a new tab-delimited file (FILEHANDLE).
	a. Using foreach loops, iterate through each level of the hash of hashes of hashes.
	b. print output to a new file called all.txt in with this format:
	"seq1\tDesc\tGC%\tA:count,T:count,C:count,T:count\tsequence\n"

Perl VIII - Modules - Problem Set
 
1. Download and install a module using CPAN
 
	$ cpan
 
	CPAN should ask if you want to configure automatically. Say YES.
	Once it's done configuring, you should get a cpan prompt like this:
 
	cpan>
 
	Type the following to install the module Math::Round:
 
	cpan> install Math::Round
 
	then, once it's installed, write a short script that uses the round() to round any numbers
	entered as arguments on the command line.
 
 
2. Take the subroutine that you created in the subroutines problem set, and make it into a module.
 
3. Modify your script from the subroutines problem set so that it now calls that subroutine from the module.
 
4. Modify the module to automatically export the subroutine by default.
 
5. (optional bonus question) Write a script to read FASTA files. Make a module with four subroutines.
 
	Each subroutine will take a FASTA sequence as input. Then, write one subroutine for each of the following:
 
	- getting the name (sequence ID) of the sequence
	- getting the description of the sequence
	- getting the sequence itself
	- reformatting the sequence to be a user-specified number of characters
	  per line