Bio::Tools::Primer3(3)User Contributed Perl DocumentatioBio::Tools::Primer3(3)NAMEBio::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\n";
# get all the results
my $all_results = $p3->all_results;
print "ALL the results\n";
foreach my $key (keys %{$all_results}) {
print "$key\t${$all_results}{$key}\n";
}
# get specific results
my $result1 = $p3->primer_results(1);
print "The first primer is\n";
foreach my $key (keys %{$result1}) {
print "$key\t${$result1}{$key}\n";
}
# 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, "\n";
DESCRIPTIONBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::Tools::Primer3(3)
