Query: bio::clusterio::dbsnp
OS: debian
Section: 3pm
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
Bio::ClusterIO::dbsnp(3pm) User Contributed Perl Documentation Bio::ClusterIO::dbsnp(3pm)NAMEBio::ClusterIO::dbsnp - dbSNP input streamSYNOPSISDo not use this module directly. Use it via the Bio::ClusterIO class.DESCRIPTIONParse 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/).FEEDBACKMailing 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/AUTHORAllen Day <allenday@ucla.edu>APPENDIXThe 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)
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