SNP.pm

- NAME
- SYNOPSIS
- DESCRIPTION
- LICENSE
- FEEDBACK
- AUTHOR - Steve Mathias
- DETAILS
- Imported Packages
- Public methods

- getSequence
- printXML
- asHTML

# NAME

Genetics::SNP

# SYNOPSIS

      $snp = new Genetics::SNP(name => 'EAEx1.1',
                               importID => 265,
                               dateCreated => $today,
                               Keywords => [ {name => "Test Data",
                                              dataType => "Boolean",
                                              value => 1},
                                           ],
                               chromosome => "12",
                               malePloidy => 2,
                               femalePloidy => 2,
                               snpType => "Substitution",
                               functionClass => "Synonymous",
                               snpIndex => 2,
                               isConfirmed => 1,
                               confirmMethod => "Resequencing",
                               comment => "Highly expressed in muscle",
                               Organism => {genusSpecies => "Homo sapiens"},
                               Alleles => [ {name => "C", type => "Nucleotide"},
                                            {name => "T", type => "Nucleotide"} ],
                               Sequence => {lengthUnits => "bp",
                                            length => 17,
                                            sequence => "ACGTUMRWSYKVHDBXN"},
                               ISCNMapLocations => [ {chrNumber => "12",
                                                      chrArm => "p",
                                                      band => "12.2",
                                                      bandingMethod => "Geimsa"},
                                                   ],
                              ) ;

    See the GenPerl Tutorial for more information.

# DESCRIPTION

SNP objects represent single nucleotide polymorphisms.

# LICENSE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

# FEEDBACK

Currently, all feedback should be sent directly to the author.

# AUTHOR - Steve Mathias

Email: mathias@genomica.com

Phone: (720) 565-4029

Address: Genomica Corporation 1745 38th Street Boulder, CO 80301

# DETAILS

The rest of the documentation describes each of the object variables and methods. The names of internal variables and methods are preceded with an underscore (_).

# Imported Packages

     Genetics::Object       Superclass
     strict                 Just to be anal
     vars                   Global variables

# Public methods

## getSequence

     Function  : Return the nucleotide sequence of a SNP object
     Arguments : N/A
     Returns   : A scalar text string
     Example   : getSequence()
     Scope     : Public Instance Method
     Comments  :

## printXML

      Function  : Print an XML representation of the object.
      Argument  : A Genetics::Subject object and the XML::Writer object being used
                  to generate the XML.
      Returns   : N/A
      Scope     : Public Instance Method
      Comments  : Calls Genetics::Object->printGeneralXML to generate XML elements
                  common to all Genetics::Object objects.

## asHTML

      Function  : Generate an HTML representation of the object.
      Argument  : A Genetics::SNP object and a scalar containing the name of the
                  GenPerl database in which the object is stored.
      Returns   : Scalar containing the HTML text.
      Scope     : Public Instance Method
      Comments  : Calls Genetics::Object->_generalHTMLParam to generate HTML
                  elements common to all Genetics::Object objects.  An
                  HTML::Template object is used to actually generate the HTML.