Provided by: libbio-perl-perl_1.6.923-1_all
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 ftp://ftp.ncbi.nih.gov/snp/).
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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)