bio::primerdesigner::primer3(3pm) [debian man page]
Bio::PrimerDesigner::primer3(3pm) User Contributed Perl Documentation Bio::PrimerDesigner::primer3(3pm) NAME
Bio::PrimerDesigner::primer3 - An class for accessing primer3 SYNOPSIS
use Bio::PrimerDesigner::primer3; METHODS
Methods are called using the simplifed alias for each primer3 result or the raw primer3 BoulderIO key. Use the raw_output method to view the raw output. binary_name Defines the binary's name on the system. check_params Make sure we have required primer3 arguments. design Build the primer3 config file, run primer3, then parse the results. Expects to be passed a hash of primer3 input options. Returns an object that can be used to call result methods. request Figures out where the primer3 binary resides and accesses it with a list of parameters for designing primers. check_results Verify the validity of the design results. list_aliases Prints a list of shorthand aliases for the primer3 BoulderIO input format. The full input/ouput options and the aliases can be used interchangeably. list_params Returns a list of primer3 configuration options. primer3 will use reasonable default options for most parameters. example Runs a sample remote primer design job. Returns an Bio::PrimerDesigner::Result object. _example_dna Returns an example DNA sequence. AUTHOR
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::epcr. perl v5.10.0 2009-08-04 Bio::PrimerDesigner::primer3(3pm)
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Bio::Tools::Primer3(3pm) User Contributed Perl Documentation Bio::Tools::Primer3(3pm) NAME
Bio::Tools::Primer3 - Create input for and work with the output from the program primer3 SYNOPSIS
# parse primer3 output to get some data # this is also called from Bio::Tools::Run::Primer3 use Bio::Tools::Primer3; # read a primer3 output file my $p3 = Bio::Tools::Primer3->new(-file=>"data/primer3_output.txt"); # how many results were there? my $num = $p3->number_of_results; print "There were $num results "; # get all the results my $all_results = $p3->all_results; print "ALL the results "; foreach my $key (keys %{$all_results}) { print "$key ${$all_results}{$key} "; } # get specific results my $result1 = $p3->primer_results(1); print "The first primer is "; foreach my $key (keys %{$result1}) { print "$key ${$result1}{$key} "; } # get the results as a Bio::Seq::PrimedSeq stream my $primer = $p3->next_primer; print "The left primer in the stream is ", $primer->get_primer('-left_primer')->seq->seq, " "; DESCRIPTION
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://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 (bioinformatics1@dieselwurks.com) I have ripped some of his code, and added a lot of my own. I hope he is not mad at me! This is probably best run in one of the two following ways: i. To parse the output from Bio::Tools::Run::Primer3. You will most likely just use next_primer to get the results from Bio::Tools::Run::Primer3. ii. To parse the output of primer3 handed to it as a file name. FEEDBACK
Mailing Lists 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 heavily on work of Chad Matsalla bioinformatics1@dieselwurks.com CONTRIBUTORS
Brian Osborne bosborne at alum.mit.edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new() Usage : my $primer3 = Bio::Tools::Primer3->new(-file=>$file) to read a primer3 output file. Function: Parse primer3 output Returns : Does not return anything. If called with a filename will allow you to retrieve the results Args : -file (optional) file of primer3 results to parse -verbose (optional) set verbose output Notes : number_of_results Title : number_of_results() Usage : $primer3->number_of_results() Function: Retrieve the number of primers returned from Primer3. Returns : A scalar Args : None Notes : This returns the count of the primers returned by Primer3 (aka how many of them there are). This is one more than the maximum offset into the zero based list of primers that is accessed by primer_results(). all_results Title : all_results() Usage : $primer3->all_results() to print all results or $primer3->all_results('primer3 result name', 'other results') to return a specific result Function: Retrieve the results returned from Primer3. Returns : A reference to a hash Args : Optional array of results to retrieve primer_results Title : primer_results() Usage : $primer3->primer_results(2) to print results for the third choice primer (indexed on 0) Function: Retrieve the results returned from Primer3 for specific primer pairs. Returns : A reference to a hash Args : A number between 0 and the maximum number of primers to retrieve _readfile Title : _readfile() Usage : $self->_readfile(); Function: An internal function that reads a file and sets up the results Returns : Nothing. Args : None Notes : next_primer Title : next_primer() Usage : while (my $primed_seq = $primer3->next_primer()) { Function: Retrieve the primed sequence and a primer pair, one at a time Returns : Returns a Bio::Seq::PrimedSeq feature, one at a time Args : None Notes : Use $primed_seq->annotated_seq to get an annotated sequence object you can write out. primer_stream Title : primer_stream() Usage : while (my $primed_seq = $primer3->primer_stream()) { Function: Retrieve the primer/sequences one at a time Returns : Returns a Bio::Seq::PrimedSeq feature, one at a time Args : None Notes : Deprecated, just a link to next_primer _separate Title : _separate() Usage : $self->_separate(); Function: An internal function that groups the results by number (e.g. primer pair 1, etc) Returns : Nothing. Args : None Notes : _set_variable Title : _set_variable() Usage : $self->_set_variable('variable name', 'value'); Function: An internal function that sets a variable Returns : Nothing. Args : None Notes : Used to set $self->{results} and $self->seqobject perl v5.14.2 2012-03-02 Bio::Tools::Primer3(3pm)