Bio::ClusterIO::dbsnp(3pm)				User Contributed Perl Documentation				Bio::ClusterIO::dbsnp(3pm)

NAME

       Bio::ClusterIO::dbsnp - dbSNP input stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::ClusterIO class.

DESCRIPTION

       Parse dbSNP XML files, one refSNP entry at a time. Note this handles dbSNPp output generated by NBCI's eutils and does NOT parse output
       derived from SNP's XML format (found at ftp://ftp.ncbi.nih.gov/snp/).

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:

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

AUTHOR

       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_cluster
	Title	: next_cluster
	Usage	: $dbsnp = $stream->next_cluster()
	Function: returns the next refSNP in the stream
	Returns : Bio::Variation::SNP object representing composite refSNP
		  and its component subSNP(s).
	Args	: NONE

   SAX methods
   start_document
	Title	: start_document
	Usage	: $parser->start_document;
	Function: SAX method to indicate starting to parse a new document.
		  Creates a Bio::Variation::SNP
	Returns : none
	Args	: none

   end_document
	Title	: end_document
	Usage	: $parser->end_document;
	Function: SAX method to indicate finishing parsing a new document
	Returns : none
	Args	: none

   start_element
	Title	: start_element
	Usage	: $parser->start_element($data)
	Function: SAX method to indicate starting a new element
	Returns : none
	Args	: hash ref for data

   end_element
	Title	: end_element
	Usage	: $parser->end_element($data)
	Function: Signals finishing an element
	Returns : none
	Args	: hash ref for data

   characters
	Title	: characters
	Usage	: $parser->characters($data)
	Function: Signals new characters to be processed
	Returns : characters read
	Args	: hash ref with the key 'Data'

   use_tempfile
	Title	: use_tempfile
	Usage	: $obj->use_tempfile($newval)
	Function: Get/Set boolean flag on whether or not use a tempfile
	Example :
	Returns : value of use_tempfile
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02						Bio::ClusterIO::dbsnp(3pm)