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bio::seqfeature::tools::idhandler(3pm) [debian man page]

Bio::SeqFeature::Tools::IDHandler(3pm)			User Contributed Perl Documentation		    Bio::SeqFeature::Tools::IDHandler(3pm)

NAME

       Bio::SeqFeature::Tools::IDHandler - maps $seq_feature->primary_tag

SYNOPSIS

	 use Bio::SeqIO;
	 use Bio::SeqFeature::Tools::IDHandler;

DESCRIPTION

       Class to map $seq_feature->primary_tag

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 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 - Chris Mungall
       Email:  cjm@fruitfly.org

APPENDIX

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

   new
	Title	: new
	Usage	: $unflattener = Bio::SeqFeature::Tools::IDHandler->new();
	Function: constructor
	Example :
	Returns : a new Bio::SeqFeature::Tools::IDHandler
	Args	: see below

   set_ParentIDs_from_hierarchy()
	Title	: set_ParentIDs_from_hierarchy()
	Usage	: $idhandler->set_ParentIDs_from_hierarchy($fholder)
	Function: populates tags Parent and ID via holder hierarchy
	Example :
	Returns :
	Args	: Bio::featureHolderI (either a SeqFeature or a Seq)

       This is mainly for GFF3 export

       GFF3 uses the tags ID and Parent to represent the feature containment hierarchy; it does NOT use the feature holder tree

       This method sets Parent (and ID for any parents not set) based on feature holder/containement hierarchy, ready for GFF3 output

   create_hierarchy_from_ParentIDs
	Title	: create_hierarchy_from_ParentIDs
	Usage	: $idhandler->set_ParentIDs_from_hierarchy($fholder)
	Function: inverse of set_ParentIDs_from_hierarchy
	Example :
	Returns : list of top SeqFeatures
	Args	:

   generate_unique_persistent_id
	Title	: generate_unique_persistent_id
	Usage	:
	Function: generates a unique and persistent identifier for this
	Example :
	Returns : value of primary_id (a scalar)
	Args	:

       Will generate an ID, and set primary_id() (see above)

       The ID is a string generated from

	 seq_id
	 primary_tag
	 start
	 end

       There are three underlying assumptions: that all the above accessors are set; that seq_id is a persistent and unique identifier for the
       sequence containing this feature; and that

	 (seq_id, primary_tag, start, end)

       is a "unique constraint" over features

       The ID is persistent, so long as none of these values change - if they do, it is considered a separate entity

perl v5.14.2							    2012-03-02				    Bio::SeqFeature::Tools::IDHandler(3pm)

Check Out this Related Man Page

Bio::SeqIO::interpro(3pm)				User Contributed Perl Documentation				 Bio::SeqIO::interpro(3pm)

NAME

       Bio::SeqIO::interpro - InterProScan XML input/output stream

SYNOPSIS

	 # do not call this module directly, use Bio::SeqIO

	 use strict;
	 use Bio::SeqIO;

	 my $io = Bio::SeqIO->new(-format => "interpro",
				  -file   => $interpro_file);

	 while (my $seq = $io->next_seq) {
	   # use the Sequence object
	 }

DESCRIPTION

       Bio::SeqIO::interpro will parse Interpro scan XML (version 1.2) and create Bio::SeqFeature::Generic objects based on the contents of the
       XML document.

       Bio::SeqIO::interpro will also attach the annotation given in the XML file to the Bio::SeqFeature::Generic objects that it creates.

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:

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

AUTHOR - Jared Fox
       Email jaredfox@ucla.edu

CONTRIBUTORS

       Allen Day allenday@ucla.edu

APPENDIX

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

   next_seq
	Title	: next_seq
	Usage	: my $seqobj = $stream->next_seq
	Function: Retrieves the next sequence from a SeqIO::interpro stream.
	Returns : A Bio::Seq::RichSeq object
	Args	:

   _initialize
	Title	: _initialize
	Usage	:
	Function:
	Returns :
	Args	:

   _sequence_factory
	Title	: _sequence_factory
	Usage	:
	Function:
	Returns :
	Args	:

   _xml_parser
	Title	: _xml_parser
	Usage	:
	Function:
	Returns :
	Args	:

   _parse_xml
	Title	: _parse_xml
	Usage	:
	Function:
	Returns :
	Args	:

   _dom
	Title	: _dom
	Usage	:
	Function:
	Returns :
	Args	:

perl v5.14.2							    2012-03-02						 Bio::SeqIO::interpro(3pm)
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