/ 
BioPerl-1.6.922
River stage two • 60 direct dependents • 65 total dependents
/ Bio::ClusterIO::dbsnp

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)