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Bio::ClusterIO::dbsnp(User Contributed Perl DocumentatBio::ClusterIO::dbsnp(3)
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:
http://bugzilla.open-bio.org/
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)
perl v5.14.1 2011-07-22 Bio::ClusterIO::dbsnp(3)
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