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://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 _

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq