GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::TOOLS::RUN::PHYLO::HYPHY::BATCHFILE (3)

.ds Aq ’

NAME

Bio::Tools::Run::Phylo::Hyphy::BatchFile - Wrapper for custom execution of Hyphy batch files

CONTENTS

SYNOPSIS

my $aln = Bio::Align::AlignI->new(); my $treeio = Bio::TreeIO->new(-format => nexus, -file => $tree_file); my $tree = $treeio->next_tree(); my $bf_exec = Bio::Tools::Run::Phylo::Hyphy::BatchFile->new(-params => {’bf’ => hyphybatchfile.bf, ’order’ => [Universal, Custom, $aln, 001001, $tree]}); $bf_exec->set_parameter(’3’, 012012); my ($rc,$parser) = $bf_exec->run();

DESCRIPTION

This module creates a generic interface to processing of HBL files in HyPhy ([Hy]pothesis Testing Using [Phy]logenies), a package by Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org for more information.

Instances of this module require only a link to the batch file and an ordered list of parameters, as described in the HyPhy documentation SelectionAnalyses.pdf.

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:



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



AUTHOR - Daisie Huang

Email daisieh@zoology.ubc.ca

CONTRIBUTORS

Additional contributors names and emails here

    valid_values



 Title   : valid_values
 Usage   : $factory->valid_values()
 Function: returns the possible parameters
 Returns:  an array holding all possible parameters. The default
values are always the first one listed.  These descriptions are
essentially lifted from the python wrapper or provided by the author.
 Args    : None



    new



 Title   : new
 Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::BatchFile->new();
 Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::BatchFile object
 Returns : Bio::Tools::Run::Phylo::Hyphy::BatchFile
 Args    : -alignment => the Bio::Align::AlignI object
           -save_tempfiles => boolean to save the generated tempfiles and
                              NOT cleanup after onesself (default FALSE)
           -tree => the Bio::Tree::TreeI object
           -params => a hashref of parameters (all passed to set_parameter)
                      this hashref should include   bf => custombatchfile.bf
                                                    order => [array of ordered parameters]
           -executable => where the hyphy executable resides



See also: Bio::Tree::TreeI, Bio::Align::AlignI

    update_ordered_parameters



 Title   : update_ordered_parameters
 Usage   : $BatchFile->update_ordered_parameters();
 Function: updates all of the parameters needed for the ordered input redirect in HBL.
 Returns : nothing
 Args    : none



    run



 Title   : run
 Usage   : my ($rc,$results) = $BatchFile->run();
 Function: run the Hyphy analysis using the specified batchfile and its ordered parameters
 Returns : Return code, Hash
 Args    : none



    create_wrapper



 Title   : create_wrapper
 Usage   : $self->create_wrapper
 Function: Creates the wrapper file for the batchfile specified in the hash, saves it to the hash as _wrapper.
 Returns : nothing
 Args    : none



    set_parameter

Title : set_parameter Usage : $hyphy->set_parameter($param,$val); Function: Sets the named parameter $param to $val if it is a non-numeric parameter
If $param is a number, sets the corresponding value of the ordered redirect array (starts from 1). Returns : boolean if set was successful Args : $param => name of the parameter
$value => value to set the parameter to

    batchfile

Title : batchfile Usage : $hyphy->batchfile($bf_name); Function: Gets/sets the batchfile that is run by $hyphy. Returns : The batchfile path. Args : $bf_name => path of new batchfile

    make_batchfile_with_contents

Title : make_batchfile_with_contents Usage : $hyphy->make_batchfile_with_contents($bf_string); Function: Creates a temporary file with the specified string of contents for the batchfile. Returns : The batchfile path. Args : $bf_string => contents for the batchfile

    set_default_parameters



 Title   : set_default_parameters
 Usage   : $BatchFile->set_default_parameters(0);
 Function: (Re)set the default parameters from the defaults
           (the first value in each array in the
            valid_values)
 Returns : none
 Args    : boolean: keep existing parameter values



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::TOOLS::RUN::PHYLO::HYPHY::BATCHFILE (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.