Provided by: libbio-perl-perl_1.6.901-2_all bug

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