SYNOPSIS
Bio::Tools::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files.This module provides a bioperl interface to the program primer3. See http://frodo.wi.mit.edu/primer3/primer3_code.html for details and to download the software. This module only works for primer3 release 1 but is not guaranteed to work with earlier versions.
# design some primers.
# the output will be put into temp.out
use Bio::Tools::Run::Primer3;
use Bio::SeqIO;
my $seqio = Bio::SeqIO->new(-file=>'data/dna1.fa');
my $seq = $seqio->next_seq;
my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq,
-outfile => "temp.out",
-path => "/usr/bin/primer3_core");
# or after the fact you can change the program_name
$primer3->program_name('my_suprefast_primer3');
unless ($primer3->executable) {
print STDERR "primer3 can not be found. Is it installed?\n";
exit(-1)
}
# what are the arguments, and what do they mean?
my $args = $primer3->arguments;
print "ARGUMENT\tMEANING\n";
foreach my $key (keys %{$args}) {print "$key\t", $$args{$key}, "\n"}
# set the maximum and minimum Tm of the primer
$primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
# design the primers. This runs primer3 and returns a
# Bio::Tools::Run::Primer3 object with the results
$results = $primer3->run;
# see the Bio::Tools::Run::Primer3 pod for
# things that you can get from this. For example:
print "There were ", $results->number_of_results, " primers\n";
Bio::Tools::Run::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files.
This module provides a bioperl interface to the program primer3. See http://www-genome.wi.mit.edu/genome_software/other/primer3.html for details and to download the software.
This module is based on one written by Chad Matsalla ([email protected]). I have ripped some of his code, and added a lot of my own. I hope he is not mad at me!
FEEDBACK
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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
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CONTRIBUTORS
Shawn Hoon shawnh-at-stanford.edu Jason Stajich jason-at-bioperl.org Brian Osborne osborne1-at-optonline.netAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new()
Title : new()
Usage : my $primer3 = Bio::Tools::Run::Primer3->new(-file=>$file) to read
a primer3 output file.
my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>sequence object)
design primers against sequence
Function: Start primer3 working and adds a sequence. At the moment it
will not clear out the old sequence, but I suppose it should.
Returns : Does not return anything. If called with a filename will allow
you to retrieve the results
Args : -seq (optional) Bio::Seq object of sequence. This is required
to run primer3 but can be added later with add_targets()
-outfile file name to output results to (can also be added
with $primer3->outfile_name
-path path to primer3 executable, including program name, e.g.
"/usr/bin/primer3_core". This can also be set with program_name
and program_dir
-verbose (optional) set verbose output
Notes :
program_name
Title : program_name Usage : $primer3->program_name() Function: holds the program name Returns: string Args : None
program_dir
Title : program_dir Usage : $primer3->program_dir($dir) Function: returns the program directory, which may also be obtained from ENV variable. Returns : string Args :
add_targets()
Title : add_targets()
Usage : $primer3->add_targets(key=>value)
Function: Add any legal value to the input command line.
Returns : Returns the number of arguments added.
Args : Use $primer3->arguments to find a list of all the values
that are allowed, or see the primer3 docs.
Notes : This will only do limited error checking at the moment,
but it should work.
run()
Title : run() Usage : $primer3->run(); Function: Run the primer3 program with the arguments that you have supplied. Returns : A Bio::Tools::Primer3 object containing the results. Args : None. Note : See the Bio::Tools::Primer3 documentation for those functions.
arguments()
Title : arguments()
Usage : $hashref = $primer3->arguments();
Function: Describes the options that you can set through Bio::Tools::Run::Primer3,
with a brief (one line) description of what they are and their
default values
Returns : A string (if an argument is supplied) or a reference to a hash.
Args : If supplied with an argument will return a string of its
description.
If no arguments are supplied, will return all the arguments as a
reference to a hash
Notes : Much of this is taken from the primer3 README file, and you should
read that file for a more detailed description.
version
Title : version Usage : $v = $prog->version(); Function: Determine the version number of the program Example : Returns : float or undef Args : none
_input_args()
Title : _input_args()
Usage : an internal method to set the input arguments for Primer3
Function: Define a hash with keys for each of the input arguments and values
as a short one line description
Returns : A reference to a hash.
Args : None.
Notes : Much of this is taken from the primer3 README file, and you should
read that file for a more detailed description.