bio::taxonomy::factoryi(3pm) [debian man page]

Bio::Taxonomy::FactoryI(3pm)				User Contributed Perl Documentation			      Bio::Taxonomy::FactoryI(3pm)

NAME

       Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy

DESCRIPTION

       NB: This module has been deprecated.

       $factory->fetch is a general method to fetch Taxonomy by either NCBI taxid or any types of names.

       $factory->fetch_parent($taxonomy), returns a Taxonomy that is one-step higher rank of the taxonomy specified as argument.

       $factory->fetch_children($taxonomy), reports an array of Taxonomy those are one-step lower rank of the taxonomy specified as the argument.

AUTHOR - Juguang Xiao
       juguang@tll.org.sg

CONTRIBUTORS

       Additional contributors' names and emails here

APPENDIX

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

   fetch
	 Title:    fetch
	 Usage:    my $taxonomy = $factory->fetch(-taxon_id => 9605);
		   my $taxonomy = $factory->fetch(-common_name => 'mammals');
	 Fuctnion: Fetch taxonomy by taxon_id, common name or scientific name.
	 Returns:  an instance of Bio::Taxonomy
	 Args:	   -taxon_id => NCBI taxonomy ID
		   -common_name => comon name, such as 'human', 'mammals'
		   -scientifc_name => specitic name, such as 'sapiens', 'Mammalia'

   fuzzy_fetch
	 Title:    fuzzy_fetch
	 Usage:    my @taxonomy = $factory->fuzzy_fetch(-name => 'mouse');
	 Function: Fuzzy fetch by name, or any text information found in DB
	 Returns:  an array reference of Bio::Taxonomy objects
	 Args:	   -name => any name, such as common name, variant, scientific name
		   -description, or -desc => any text information

   fetch_parent
	 Title:    fetch_parent
	 Usage:    my $parent_taxonomy = $factory->fetch_parent($taxonomy);
	 Function: Fetch the parent that is one-rank higher than the argument.
	 Returns:  an instance of Bio::Taxonomy, or undef if the arg is the top one.
	 Args:	   a Bio::Taxonomy object.

   fetch_children
	 Title:    fetch_children
	 Usage:    my @children_taxonomy = $factory->fetch_children($taxonomy);
	 Function: Fetch all children those are one-rank lower than the argument.
	 Returns:  an array reference of Bio::Taxonomy objects
	 Args:	   a Bio::Taxonomy object.

perl v5.14.2							    2012-03-02					      Bio::Taxonomy::FactoryI(3pm)

Bio::Tools::Run::Profile(3pm)				User Contributed Perl Documentation			     Bio::Tools::Run::Profile(3pm)

NAME

       Bio::Tools::Run::Profile

SYNOPSIS

	Build a Profile factory
	# $paramfile is the full path to the seg binary file

	my @params = ('DB',$dbfile,'PROGRAM',$paramfile);
	my $factory = Bio::Tools::Run::Profile->new($param);

	# Pass the factory a Bio::PrimarySeqI object
	# @feats is an array of Bio::SeqFeature::Generic objects
	my @feats = $factory->run($seq);

DESCRIPTION

	Wrapper module for the pfscan program

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

AUTHOR - Balamurugan Kumarasamy
	Email: fugui@worf.fugu-sg.org

APPENDIX

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

   program_name
	Title	: program_name
	Usage	: $factory>program_name()
	Function: holds the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns:  string
	Args	:

   new
	Title	: new
	Usage	: my $factory= Bio::Tools::Run::Profile->new($param);
	Function: creates a new Profile factory
	Returns:  Bio::Tools::Run::Profile
	Args	:

   predict_protein_features
	Title	:   predict_protein_features
	Usage	:   DEPRECATED. Use $factory->run($seq) instead.
	Function:   Runs Profile and creates an array of featrues
	Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
	Args	:   A Bio::PrimarySeqI

   run
	Title	:   run
	Usage	:   my @feats = $factory->run($seq)
	Function:   Runs Profile
	Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
	Args	:   A Bio::PrimarySeqI

   _input
	Title	:   _input
	Usage	:   $factory->_input($seqFile)
	Function:   get/set for input file
	Returns :
	Args	:

   _run
	Title	:   _run
	Usage	:   $factory->_run()
	Function:   Makes a system call and runs pfscan
	Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
	Args	:

   _writeSeqFile
	Title	:   _writeSeqFile
	Usage	:   $factory->_writeSeqFile($seq)
	Function:   Creates a file from the given seq object
	Returns :   A string(filename)
	Args	:   Bio::PrimarySeqI

perl v5.12.3							    2011-06-18					     Bio::Tools::Run::Profile(3pm)