Genetics::Marker
$marker = new Genetics::Marker(name => 'D12S91',
importID => 1,
dateCreated => $today,
comment => "Marker in EA critical region",
NameAliases => [ {name => "d12s6666"}
],
Contact => {name => "Jean Weissenbach",
organization => "Genethon"},
DBXReferences => [ {accessionNumber => "NT_009758.3",
databaseName => "GenBank"}
],
Keywords => [ {name => "Test Data",
dataType => "Boolean",
value => 1},
],
chromosome => "12",
malePloidy => 2,
femalePloidy => 2,
polymorphismType => "Repeat",
polymorphismIndex1 => 7,
polymorphismIndex2 => 11,
repeatSequence => "CA",
Organism => {genusSpecies => "Homo sapiens"},
Alleles => [ {name => 1, type => "Code"},
{name => 2, type => "Code"},
{name => 3, type => "Code"},
{name => 4, type => "Code"},
{name => 5, type => "Code"},
{name => 6, type => "Code"} ],
ISCNMapLocations => [ {chrNumber => "12",
chrArm => "p",
band => "12.2.1",
bandingMethod => "Geimsa"}, ],
Sequence => {lengthUnits => "bp",
length => 17,
sequence => "ACGTUMRCACAWSYKVHDBXN"},
) ;
See the GenPerl Tutorial for more information.
Marker objects represent polymorphic genetic markers.
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
Currently, all feedback should be sent directly to the author.
Email: mathias@genomica.com
Phone: (720) 565-4029
Address: Genomica Corporation 1745 38th Street Boulder, CO 80301
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 (_).
Genetics::Object Superclass strict Just to be anal vars Global variables
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.
Function : Generate an HTML representation of the object.
Argument : A Genetics::Marker 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.