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Manual Reference Pages  -  BIO::CLUSTERIO::DBSNP (3)

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NAME

Bio::ClusterIO::dbsnp - dbSNP input stream

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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)



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perl v5.20.3 BIO::CLUSTERIO::DBSNP (3) 2016-04-05

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