Bio::ClusterIO::dbsnp - dbSNP input stream


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


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


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


 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


 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


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


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


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


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


 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)