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://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)