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.IX Title "Bio::ClusterIO::dbsnp 3pm"
.TH Bio::ClusterIO::dbsnp 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::ClusterIO::dbsnp \- dbSNP input stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this module directly.  Use it via the Bio::ClusterIO class.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Parse dbSNP \s-1XML\s0 files, one refSNP entry at a time. Note this handles dbSNPp
output generated by \s-1NBCI\s0's eutils and does \s-1NOT\s0 parse output derived from
\&\s-1SNP\s0's \s-1XML\s0 format (found at ftp://ftp.ncbi.nih.gov/snp/).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Allen Day <allenday@ucla.edu>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "next_cluster"
.IX Subsection "next_cluster"
.Vb 6
\& 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
.Ve
.SS "\s-1SAX\s0 methods"
.IX Subsection "SAX methods"
.SS "start_document"
.IX Subsection "start_document"
.Vb 6
\& 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
.Ve
.SS "end_document"
.IX Subsection "end_document"
.Vb 5
\& Title   : end_document
\& Usage   : $parser\->end_document;
\& Function: SAX method to indicate finishing parsing a new document
\& Returns : none
\& Args    : none
.Ve
.SS "start_element"
.IX Subsection "start_element"
.Vb 5
\& Title   : start_element
\& Usage   : $parser\->start_element($data)
\& Function: SAX method to indicate starting a new element
\& Returns : none
\& Args    : hash ref for data
.Ve
.SS "end_element"
.IX Subsection "end_element"
.Vb 5
\& Title   : end_element
\& Usage   : $parser\->end_element($data)
\& Function: Signals finishing an element
\& Returns : none
\& Args    : hash ref for data
.Ve
.SS "characters"
.IX Subsection "characters"
.Vb 5
\& Title   : characters
\& Usage   : $parser\->characters($data)
\& Function: Signals new characters to be processed
\& Returns : characters read
\& Args    : hash ref with the key \*(AqData\*(Aq
.Ve
.SS "use_tempfile"
.IX Subsection "use_tempfile"
.Vb 6
\& 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)
.Ve