bio::primerdesigner(3pm) [debian man page]

Bio::PrimerDesigner(3pm)				User Contributed Perl Documentation				  Bio::PrimerDesigner(3pm)

NAME

       Bio::PrimerDesigner - Design PCR Primers using primer3 and epcr

SYNOPSIS

	 use Bio::PrimerDesigner;

	 my $pd = Bio::PrimerDesigner->new;

	 #
	 # Define the DNA sequence, etc.
	 #
	 my $dna   = "CGTGC...TTCGC";
	 my $seqID = "sequence 1";

	 #
	 # Define design parameters (native primer3 syntax)
	 #
	 my %params = (
	     PRIMER_NUM_RETURN	 => 2,
	     PRIMER_SEQUENCE_ID  => $seqID,
	     SEQUENCE		 => $dna,
	     PRIMER_PRODUCT_SIZE => '500-600'
	 );

	 #
	 # Or use input aliases
	 #
	 %param = (
	     num		 => 2,
	     id 		 => $seqID,
	     seq		 => $dna,
	     sizerange		 => '500-600'
	 );

	 #
	 # Design primers
	 #
	 my $results = $pd->design( %params ) or die $pd->error;

	 #
	 # Make sure the design was successful
	 #
	 if ( !$results->left ) {
	     die "No primers found
", $results->raw_data;
	 }

	 #
	 # Get results (single primer set)
	 #
	 my $left_primer  = $results->left;
	 my $right_primer = $results->right;
	 my $left_tm	  = $results->lefttm;

	 #
	 # Get results (multiple primer sets)
	 #
	 my @left_primers  = $results->left(1..3);
	 my @right_primers = $results->right(1..3);
	 my @left_tms	   = $results->lefttm(1..3);

DESCRIPTION

       Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results.
       Because primer3 and e-PCR are only available for Unix-like operating systems, Bio::PrimerDesigner offers the ability to accessing the
       primer3 binary via a remote server.  Local installations of primer3 or e-PCR on Unix hosts are also supported.

METHODS

   binary_path
       Gets/sets path to the primer3 binary.

   design
       Makes the primer design or e-PCR request.  Returns an Bio::PrimerDesigner::Result object.

   epcr_example
       Run test e-PCR job.  Returns an Bio::PrimerDesigner::Results object.

   list_aliases
       Lists aliases for primer3 input/output options

   list_params
       Lists input options for primer3 or epcr, depending on the context

   method
       Gets/sets method of accessing primer3 or epcr binaries.

   os_is_unix
       Returns 1 if it looks like the operating system is a Unix variant, otherwise returns 0.

   primer3_example
       Runs a sample design job for primers.  Returns an Bio::PrimerDesigner::Results object.

   program
       Gets/sets which program to use.

   run
       Alias to "design."

   url
       Gets/sets the URL for accessing the remote binaries.

   verify
       Tests local installations of primer3 or e-PCR to ensure that they are working properly.

AUTHORS

       Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.

LICENSE

       This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
       the Free Software Foundation; version 3 or any later version.

       This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

       You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation,
       Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

SEE ALSO

       Bio::PrimerDesigner::primer3, Bio::PrimerDesigner::epcr.

perl v5.10.0							    2009-08-04						  Bio::PrimerDesigner(3pm)

Bio::Seq::PrimedSeq(3pm)				User Contributed Perl Documentation				  Bio::Seq::PrimedSeq(3pm)

NAME

       Bio::Seq::PrimedSeq - A representation of a sequence and two primers flanking a target region

SYNOPSIS

	 # The easiest way to use this is probably either, (i), get the
	 # output from Bio::Tools::Run::Primer3, Bio::Tools::Primer3, or
	 # Bio::Tools::PCRSimulation:

	     # For example, start with a fasta file
	     use Bio::SeqIO;
	     use Bio::Tools::Run::Primer3;

	     my $file = shift || die "need a file to read";
	     my $seqin = Bio::SeqIO->new(-file => $file);
	     my $seq = $seqin->next_seq;

	     # use primer3 to design some primers
	     my $primer3run = Bio::Tools::Run::Primer3->new(-seq => $seq);
	     $primer3run -> run; # run it with the default parameters

	     # create a file to write the results to
	     my $seqout = Bio::SeqIO->new(-file => ">primed_sequence.gbk",
					  -format => 'genbank');

	     # now just get all the results and write them out.
	     while (my $results = $primer3run->next_primer) {
		$seqout->write_seq($results->annotated_seq);
	     }

	 # Or, (ii), to create a genbank file for a sequence and its cognate
	 # primers:

	    use Bio::SeqIO;
	    use Bio::Seq::PrimedSeq;

	    # have a sequence file ($file) with the template, and two primers
	    # that match it, in fasta format

	    my $file = shift || die "$0 <file>";
	    my $seqin = Bio::SeqIO->new(-file => $file);

	    # read three sequences
	    my ($template, $leftprimer, $rightprimer) =
		  ($seqin->next_seq, $seqin->next_seq, $seqin->next_seq);
	    # set up the primed sequence object
	    my $primedseq = Bio::Seq::PrimedSeq->new(-seq => $template,
						     -left_primer => $leftprimer,
						     -right_primer => $rightprimer);
	    # open a file for output
	    my $seqout = Bio::SeqIO->new(-file => ">primed_sequence.gbk",
					 -format => 'genbank');
	    # print the sequence out
	    $seqout->write_seq($primedseq->annotated_sequence);

	 # This should output a genbank file with the two primers labeled.

DESCRIPTION

       This module is a slightly glorified capsule containing a primed sequence.  It was created to address the fact that a primer is more than a
       seqfeature and there need to be ways to represent the primer-sequence complex and the behaviors and attributes that are associated with the
       complex.

       The primers are represented as Bio::SeqFeature::Primer objects, and should be instantiated first.

       A simple way to create a PrimedSeq object is as follows:

	 my $primedseq = Bio::Seq::PrimedSeq->new(
		 -seq	       => $seq,  # Bio::Seq object,
		 -left_primer  => $left, # Bio::SeqFeature::Primer object,
		 -right_primer => $right # Bio::SeqFeature::Primer object,
	 );

       From the PrimedSeq object you should be able to retrieve information about melting temperatures and what not on each of the primers and the
       amplicon.

       This is based on the PrimedSeq.pm module started by Chad Matsalla, with additions/improvements by Rob Edwards.

FEEDBACK

       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Rob Edwards, redwards@utmem.edu

       Based on a module written by Chad Matsalla, bioinformatics1@dieselwurks.com

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   new
	Title	: new()
	Usage	: $primed_sequence = Bio::SeqFeature::Primer->new(
					    -seq => $sequence,
					    -left_primer => $left_primer,
					    -right_primer => $right_primer);
	Function: A constructor for an object representing a primed sequence
	Returns : A Bio::Seq::PrimedSeq object
	Args	:  -seq => a Bio::Seq object (required)
		   -left_primer => a Bio::SeqFeature::Primer object (required)
		   -right_primer => a Bio::SeqFeature::Primer object (required)

		  Many other parameters can be included including all of the output
		  parameters from the primer3 program. At the moment most of these
		  parameters will not do anything.

   get_primer
	Title	: get_primer();
	Usage	: $primer = $primedseq->get_primer(l, left, left_primer,
		  -left_primer) to return the left primer or
		       $primer = $primedseq->get_primer(r, right, right_primer,
		  -right_primer) to return the right primer or
		       $primer = $primedseq->get_primer(b, both, both_primers,
		  -both_primers)
		  to return the left primer, right primer array
	Function: A getter for the left primer in thie PrimedSeq object.
	Returns : A Bio::SeqFeature::Primer object
	Args	: Either of (l, left, left_primer, -left_primer) to get left
		  primer.
		  Either of (r, right, right_primer, -right_primer) to get
		  right primer
		       Either of (b, both, both_primers, -both_primers) to get
		  both primers.
		  Note that this is plural. [default]

   annotated_sequence
	Title	: annotated_sequence
	Usage	: $annotated_sequence_object = $primedseq->annotated_sequence()
	Function: Get an annotated sequence object containg the left and right
		  primers
	Returns : An annotated sequence object or 0 if not defined.
	Args	:
	Note	: Use this method to return a sequence object that you can write
		  out (e.g. in GenBank format). See the example above.

   amplicon
	Title	: amplicon
	Usage	: my $amplicon = $primedseq->amplicon()
	Function: Retrieve the amplicon as a sequence object
	Returns : A seq object. To get the sequence use $amplicon->seq
	Args	: None
	Note	:

   seq
	Title	: seq
	Usage	: my $seqobj = $primedseq->seq()
	Function: Retrieve the target sequence as a sequence object
	Returns : A seq object. To get the sequence use $seqobj->seq
	Args	: None
	Note	:

   _place_seqs
	Title	: _place_seqs
	Usage	: $self->_place_seqs()
	Function: An internal method to place the primers on the sequence and
		  set up the ranges of the sequences
	Returns : Nothing
	Args	: None
	Note	: Internal use only

   _set_seqfeature
	Title	: _set_seqfeature
	Usage	: $self->_set_seqfeature()
	Function: An internal method to create Bio::SeqFeature::Generic objects
		  for the primed seq
	Returns : Nothing
	Args	: None
	Note	: Internal use only. Should only call this once left and right
		  primers have been placed on the sequence. This will then set
		  them as sequence features so hopefully we can get a nice output
		  with write_seq.

perl v5.14.2							    2012-03-02						  Bio::Seq::PrimedSeq(3pm)