Bio::ClusterIO::dbsnp(3pm) User Contributed Perl Documentation Bio::ClusterIO::dbsnp(3pm)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)
perl v5.14.2 2012-03-02 Bio::ClusterIO::dbsnp(3pm)
Check Out this Related Man Page
Bio::Variation::SNP(3pm) User Contributed Perl Documentation Bio::Variation::SNP(3pm)NAME
Bio::Variation::SNP - submitted SNP
SYNOPSIS
$SNP = Bio::Variation::SNP->new ();
DESCRIPTION
Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs,
batch IDs, validation methods).
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 _
get/set-able methods
Usage : $is = $snp->method()
Function: for getting/setting attributes
Returns : a value. probably a scalar.
Args : if you're trying to set an attribute, pass in the new value.
Methods:
--------
id
type
observed
seq_5
seq_3
ncbi_build
ncbi_chr_hits
ncbi_ctg_hits
ncbi_seq_loc
ucsc_build
ucsc_chr_hits
ucsc_ctg_hits
heterozygous
heterozygous_SE
validated
genotype
handle
batch_id
method
locus_id
symbol
mrna
protein
functional_class
is_subsnp
Title : is_subsnp
Usage : $is = $snp->is_subsnp()
Function: returns 1 if $snp is a subSNP
Returns : 1 or undef
Args : NONE
subsnp
Title : subsnp
Usage : $subsnp = $snp->subsnp()
Function: returns the currently active subSNP of $snp
Returns : Bio::Variation::SNP
Args : NONE
add_subsnp
Title : add_subsnp
Usage : $subsnp = $snp->add_subsnp()
Function: pushes the previous value returned by subsnp() onto a stack,
accessible with each_subsnp().
Sets return value of subsnp() to a new Bio::Variation::SNP
object, and returns that object.
Returns : Bio::Varitiation::SNP
Args : NONE
each_subsnp
Title : each_subsnp
Usage : @subsnps = $snp->each_subsnp()
Function: returns a list of the subSNPs of a refSNP
Returns : list
Args : NONE
perl v5.14.2 2012-03-02 Bio::Variation::SNP(3pm)