NAME¶
Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic
variant of the OMIM database
SYNOPSIS¶
use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
$av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number => ".0001",
-title => "ALCOHOL INTOLERANCE",
-symbol => "ALDH2*2",
-description => "The ALDH2*2-encoded ...",
-aa_ori => "GLU",
-aa_mut => "LYS",
-position => 487,
-additional_mutations => "IVS4DS, G-A, +1" );
DESCRIPTION¶
This class models the allelic variant of the OMIM database. This class is
intended to be used together with a OMIM entry class.
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¶
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW:
http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
APPENDIX¶
The rest of the documentation details each of the object methods.
new¶
Title : new
Usage : $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number => ".0001",
-title => "ALCOHOL INTOLERANCE",
-symbol => "ALDH2*2",
-description => "The ALDH2*2-encoded ...",
-aa_ori => "GLU",
-aa_mut => "LYS",
-position => 487,
-additional_mutations => "IVS4DS, G-A, +1" );
Function: Creates a new OMIMentryAllelicVariant object.
Returns : A new OMIMentryAllelicVariant object.
Args : -number => the OMIM allelic variant number
-title => the title
-symbol => a symbol
-description => a description
-aa_ori => the original amino acid
-aa_mut => the mutated amino acid
-position => the position of the mutation
-additional_mutations => free form description of additional mutations
init¶
Title : init()
Usage : $av->init();
Function: Initializes this OMIMentryAllelicVariant to all "".
Returns :
Args :
number¶
Title : number
Usage : $av->number( ".0001" );
or
print $av->number();
Function: Set/get for the OMIM allelic variant number of this
OMIMentryAllelicVariant.
Returns : The OMIM allelic variant number.
Args : The OMIM allelic variant number (optional).
title¶
Title : title
Usage : $av->title( "ALCOHOL INTOLERANCE" );
or
print $av->title();
Function: Set/get for the title of this OMIMentryAllelicVariant.
Returns : The title.
Args : The title (optional).
symbol¶
Title : symbol
Usage : $av->symbol( "ALDH2*2" );
or
print $av->symbol();
Function: Set/get for the symbol of this OMIMentryAllelicVariant.
Returns : A symbol.
Args : A symbol (optional).
description¶
Title : description
Usage : $av->description( "The ALDH2*2-encoded protein has a change ..." );
or
print $av->description();
Function: Set/get for the description of this OMIMentryAllelicVariant.
Returns : A description.
Args : A description (optional).
aa_ori¶
Title : aa_ori
Usage : $av->aa_ori( "GLU" );
or
print $av->aa_ori();
Function: Set/get for the original amino acid(s).
Returns : The original amino acid(s).
Args : The original amino acid(s) (optional).
aa_mut¶
Title : aa_mut
Usage : $av->aa_mut( "LYS" );
or
print $av->aa_mut();
Function: Set/get for the mutated amino acid(s).
Returns : The mutated amino acid(s).
Args : The mutated amino acid(s) (optional).
position¶
Title : position
Usage : $av->position( 487 );
or
print $av->position();
Function: Set/get for the position of the mutation.
Returns : The position of the mutation.
Args : The position of the mutation (optional).
additional_mutations¶
Title : additional_mutations
Usage : $av->additional_mutations( "1-BP DEL, 911T" );
or
print $av->additional_mutations();
Function: Set/get for free form description of (additional) mutation(s).
Returns : description of (additional) mutation(s).
Args : description of (additional) mutation(s) (optional).
to_string¶
Title : to_string()
Usage : print $av->to_string();
Function: To string method for OMIMentryAllelicVariant objects.
Returns : A string representations of this OMIMentryAllelicVariant.
Args :