Bio::Phenotype::OMIM::OMIMentryAllelicVariant.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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    :