Bio::Tools::Run::Phylo::PhyloBase man page on Fedora

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Bio::Tools::Run::PhyloUseryContributed PerBio::Tools::Run::Phylo::PhyloBase(3)

NAME
       Bio::Tools::Run::Phylo::PhyloBase- base module for phylo wrappers

SYNOPSIS
	 use base qw(Bio::Tools::Run::Phylo::PhyloBase);

DESCRIPTION
       For use by Bio::Tools::Run::Phylo modules as a base in place of
       Bio::Tools::Run::WrapperBase.

       This is based on WrapperBase but provides additional phylo-related
       private helper subs.

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://bugzilla.open-bio.org/

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

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

   _alignment
	Title	: _alignment
	Usage	: $aln = $obj->_alignment()
	Function: Get/set an alignment object, generating one from a file if desired.
	Returns : Bio::Align::AlignI (probably a Bio::SimpleAlign)
	Args	: none to get
		  OR filename & input format of the alignment file (latter defaults to
		  guess) to set from file
		  OR Bio::Align::AlignI to set

   _write_alignment
	Title	: _write_alignment
	Usage	: $obj->_write_alignment()
	Function: Writes the alignment object returned by _alignment() out in the
		  desired format to a temp file.
	Returns : filename
	Args	: string to desribe format (default 'fasta'), any other options to pass
		  to AlignIO

   _tree
	Title	: _tree
	Usage	: $tree = $obj->_tree()
	Function: Get/set a tree object, generating one from a file/database if desired
	Returns : Bio::Tree::TreeI
	Args	: none to get, OR to set:
		  OR filename & input format of the tree file (latter defaults to
		  guess) to set from file
		  OR Bio::Tree::TreeI
		  OR Bio::DB::Taxonomy when _alignment() has been set and where
		  sequences in the alignment have ids matching species in the taxonomy
		  database

   _write_tree
	Title	: _write_tree
	Usage	: $obj->_write_tree()
	Function: Writes the tree object returned by _tree() out in the desired format
		  to a temp file.
	Returns : filename
	Args	: string to desribe format (default 'newick')

   _get_seq_names
	Title	: _get_seq_names
	Usage	: @names = $obj->_get_seq_names()
	Function: Get all the sequence names (from id()) of the sequenes in the
		  alignment.  _alignment() must be set prior to calling this.
	Returns : list of strings (seq ids)
	Args	: none

   _get_node_names
	Title	: _get_node_names
	Usage	: @names = $obj->_get_node_names()
	Function: Get all the node names (from id()) of the nodes in the tree.
		  _tree must be set prior to calling this.
	Returns : list of strings (node ids)
	Args	: none

   _check_names
	Title	: _check_names
	Usage	: if ($obj->_check_names) { ... }
	Function: Determine if all sequences in the alignment file have a corresponding
		  node in the tree file. _alignment() and _tree() must be set
		  prior to calling this.
	Returns : boolean (will also warn about the specific problems when returning
		  false)
	Args	: none

perl v5.14.1			  2011-07-Bio::Tools::Run::Phylo::PhyloBase(3)
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