Bio::Variation::SNP.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   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 _

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