#
# BioPerl module for Bio::Phenotype::OMIM::OMIMentry
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian
Inheritance in Man) database entries
=head1 SYNOPSIS
$obj = Bio::Phenotype::OMIM::OMIMentry->new( -mim_number => 200000,
-description => "This is ...",
-more_than_two_genes => 1 );
=head1 DESCRIPTION
Inherits from Bio::Phenotype::PhenotypeI.
Bio::Phenotype::OMIM::OMIMparser parses the flat file representation
of OMIM (i.e. files "omim.txt" and "genemap") returning OMIMentry objects.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 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
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Phenotype::OMIM::OMIMentry;
use strict;
use Bio::Phenotype::OMIM::MiniMIMentry;
use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
use constant TRUE => 1;
use constant FALSE => 0;
use constant DEFAULT_MIM_NUMER => 0;
use base qw(Bio::Phenotype::Phenotype);
=head2 new
Title : new
Usage : $obj = Bio::Phenotype::OMIM::OMIMentry->new( -mim_number => 200000,
-description => "This is ...",
-more_than_two_genes => 1 );
Function: Creates a new OMIMentry object.
Returns : A new OMIMentry object.
Args : -mim_number => the MIM number
-title => the title or name
-alternative_titles_and_symbols => the "alternative titles and symbols"
-more_than_two_genes => can phenotype can be caused by mutation in any of two or more genes?
-is_separate => is this phenotype separate from those represented by other entries
-description => the description of this phenotype
-mapping_method => the mapping method
-gene_status => the gene status of this
-comment => a comment
-species => ref to the the species (human)
-created => created by whom/when
-edited => edited by whom/when
-contributors => contributed by whom/when
-additional_references => "see also"
-clinical_symptoms => the clinical symptoms
-minimim => the Mini MIM associated with this OMIM antry
=cut
sub new {
my( $class,@args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $mim_number,
$title,
$alternative_titles_and_symbols,
$more_than_two_genes,
$is_separate,
$description,
$mapping_method,
$gene_status,
$comment,
$species,
$created,
$edited,
$contributors,
$additional_references,
$clinical_symptoms,
$miniMIM )
= $self->_rearrange( [ qw( MIM_NUMBER
TITLE
ALTERNATIVE_TITLES_AND_SYMBOLS
MORE_THAN_TWO_GENES
IS_SEPARATE
DESCRIPTION
MAPPING_METHOD
GENE_STATUS
COMMENT
SPECIES
CREATED
EDITED
CONTRIBUTORS
ADDITIONAL_REFERENCES
CLINICAL_SYMPTOMS
MINIMIM ) ], @args );
$self->init();
$mim_number && $self->MIM_number( $mim_number );
$title && $self->title( $title );
$alternative_titles_and_symbols && $self->alternative_titles_and_symbols( $alternative_titles_and_symbols );
$more_than_two_genes && $self->more_than_two_genes( $more_than_two_genes );
$is_separate && $self->is_separate( $is_separate );
$description && $self->description( $description );
$mapping_method && $self->mapping_method( $mapping_method );
$gene_status && $self->gene_status( $gene_status );
$comment && $self->comment( $comment );
$species && $self->species( $species );
$created && $self->created( $created );
$edited && $self->edited( $edited );
$contributors && $self->contributors( $contributors );
$additional_references && $self->additional_references( $additional_references );
$clinical_symptoms && $self->clinical_symptoms_raw( $clinical_symptoms );
$miniMIM && $self->miniMIM( $miniMIM );
return $self;
} # new
=head2 init
Title : init()
Usage : $obj->init();
Function: Initializes this OMIMentry to all "" and empty lists.
Returns :
Args :
=cut
sub init {
my( $self ) = @_;
$self->MIM_number( DEFAULT_MIM_NUMER );
$self->title( "" );
$self->alternative_titles_and_symbols( "" );
$self->more_than_two_genes( FALSE );
$self->is_separate( FALSE );
$self->description( "" );
$self->mapping_method( "" );
$self->gene_status( "" );
$self->comment( "" );
my $species = Bio::Species->new();
$species->classification( qw( sapiens Homo ) );
$self->species( $species );
$self->created( "" );
$self->edited( "" );
$self->contributors( "" );
$self->additional_references( "" );
$self->clinical_symptoms( {} );
$self->remove_Correlates();
$self->remove_References();
$self->remove_AllelicVariants();
$self->remove_CytoPositions();
$self->remove_gene_symbols();
$self->remove_Genotypes();
$self->remove_DBLinks();
$self->remove_keywords();
$self->remove_Variants();
$self->remove_Measures();
$self->miniMIM( Bio::Phenotype::OMIM::MiniMIMentry->new() );
} # init
sub to_string {
my( $self ) = @_;
my $s = "";
$s .= "-- MIM number:\n";
$s .= $self->MIM_number()."\n\n";
$s .= "-- Title:\n";
$s .= $self->title()."\n\n";
$s .= "-- Alternative Titles and Symbols:\n";
$s .= $self->alternative_titles_and_symbols()."\n\n";
$s .= "-- Can be caused by Mutation in any of two or more Genes:\n";
$s .= $self->more_than_two_genes()."\n\n";
$s .= "-- Phenotype is separate:\n";
$s .= $self->is_separate()."\n\n";
$s .= "-- Description:\n";
$s .= $self->description()."\n\n";
$s .= "-- Species:\n";
$s .= $self->species()->binomial()."\n\n";
$s .= "-- Clinical Symptoms:\n";
$s .= $self->clinical_symptoms()."\n\n";
$s .= "-- Allelic Variants:\n";
$s .= $self->_array_to_string( $self->each_AllelicVariant() )."\n";
$s .= "-- Cyto Positions:\n";
$s .= $self->_array_to_string( $self->each_CytoPosition() )."\n";
$s .= "-- Gene Symbols:\n";
$s .= $self->_array_to_string( $self->each_gene_symbol() )."\n";
$s .= "-- Correlates:\n";
$s .= $self->_array_to_string( $self->each_Correlate() )."\n";
$s .= "-- References:\n";
$s .= $self->_array_to_string( $self->each_Reference() )."\n";
$s .= "-- Additional References:\n";
$s .= $self->additional_references()."\n\n";
$s .= "-- Mapping Method:\n";
$s .= $self->mapping_method()."\n\n";
$s .= "-- Gene status:\n";
$s .= $self->gene_status()."\n\n";
$s .= "-- Created:\n";
$s .= $self->created()."\n\n";
$s .= "-- Contributors:\n";
$s .= $self->contributors()."\n\n";
$s .= "-- Edited:\n";
$s .= $self->edited()."\n\n";
$s .= "-- Comment:\n";
$s .= $self->comment()."\n\n";
$s .= "-- MiniMIM:\n";
$s .= $self->miniMIM()->to_string()."\n\n";
return $s;
} # to_string
=head2 MIM_number
Title : MIM_number
Usage : $omim->MIM_number( "100050" );
or
print $omim->MIM_number();
Function: Set/get for the MIM number of this OMIM entry.
Returns : The MIM number [an integer larger than 100000].
Args : The MIM number [an integer larger than 100000] (optional).
=cut
sub MIM_number {
my ( $self, $value ) = @_;
if ( defined $value ) {
if ( $value =~ /\D/
|| ( $value < 100000 && $value != DEFAULT_MIM_NUMER ) ) {
$self->throw( "Found [$value]"
. " where [integer larger than 100000] expected" );
}
$self->{ "_MIM_number" } = $value;
}
return $self->{ "_MIM_number" };
} # MIM_number
=head2 title
Title : title
Usage : $omim->title( "AARSKOG SYNDROME" );
or
print $omim->title();
Function: Set/get for the title or name of this OMIM entry.
This method is an alias to the method "name" of
Bio::Phenotype::PhenotypeI.
Returns : The title [scalar].
Args : The title [scalar] (optional).
=cut
sub title {
my $self = shift;
$self->name(@_);
} # title
=head2 alternative_titles_and_symbols
Title : alternative_titles_and_symbols
Usage : $omim->alternative_titles_and_symbols( "AORTIC ANEURYSM, ABDOMINAL" );
or
print $omim->alternative_titles_and_symbols();
Function: Set/get for the "alternative titles and symbols" of this OMIM entry.
Currently, everything after the first line of title (TI) field is
considered "alternative titles and symbols".
Returns : "alternative titles and symbols" [scalar].
Args : "alternative titles and symbols" [scalar] (optional).
=cut
sub alternative_titles_and_symbols {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_alternative_titles_and_symbols" } = $value;
}
return $self->{ "_alternative_titles_and_symbols" };
} # alternative_titles_and_symbols
=head2 more_than_two_genes
Title : more_than_two_genes
Usage : $omim->more_than_two_genes( 1 );
or
print $omim->more_than_two_genes();
Function: This is true if this phenotype can be caused
by mutation in any of two or more genes.
In OMIM, this is indicated by a number symbol (#)
before an entry number (e.g. #114480 -- BREAST CANCER).
Returns : [1 or 0].
Args : [1 or 0] (optional).
=cut
sub more_than_two_genes {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_is_true_or_false( $value );
$self->{ "_more_than_two_genes" } = $value;
}
return $self->{ "_more_than_two_genes" };
} # more_than_two_genes
=head2 is_separate
Title : is_separate
Usage : $omim->is_separate( 1 );
or
print $omim->is_separate();
Function: This is true if the phenotype determined by the gene at
the given locus is separate from those represented by
other entries where "is_separate" is true and if the mode
of inheritance of the phenotype has been proved
(in the judgment of the authors and editors).
In OMIM, this is indicated by a asterisk (*)
before an entry number (e.g. *113705 BREAST CANCER,
TYPE 1; BRCA1).
Returns : [1 or 0].
Args : [1 or 0] (optional).
=cut
sub is_separate {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_is_true_or_false( $value );
$self->{ "_is_separate" } = $value;
}
return $self->{ "_is_separate" };
} # is_separate
=head2 mapping_method
Title : mapping_method
Usage : $omim->mapping_method( "PCR of somatic cell hybrid DNA" );
or
print $omim->mapping_method();
Function: Set/get for the mapping method of this OMIM entry.
Returns : The mapping method [scalar].
Args : The mapping method [scalar] (optional).
=cut
sub mapping_method {
my $self = shift;
return $self->{ "_mapping_method" } = shift if(@_);
return $self->{ "_mapping_method" };
} # mapping_method
=head2 gene_status
Title : gene_status
Usage : $omim->gene_status( "C" );
or
print $omim->gene_status();
Function: Set/get for the gene status of this OMIM entry.
The certainty with which assignment of loci to chromosomes or the linkage
between two loci has been established has been graded into the following
classes:
<L>C = confirmed - observed in at least two laboratories or in several families.
<L>P = provisional - based on evidence from one laboratory or one family.
<L>I = inconsistent - results of different laboratories disagree.
<L>L = limbo - evidence not as strong as that provisional, but included for
heuristic reasons. (Same as `tentative'.)
Returns : [C, P, I, or L].
Args : [C, P, I, or L] (optional).
=cut
sub gene_status {
my ( $self, $value ) = @_;
if ( defined $value ) {
#unless ( $value eq "C"
# || $value eq "P"
# || $value eq "I"
# || $value eq "L"
# || $value eq "A" # !?
# || $value eq "H" # !?
# || $value eq "U" # !?
# || $value eq "" ) {
# $self->throw( "Found [$value]"
# . " where [C, P, I, or L] expected" );
#}
unless ( $value eq "C"
|| $value eq "P"
|| $value eq "I"
|| $value eq "L"
|| $value eq "" ) {
$value = "";
}
$self->{ "_gene_status" } = $value;
}
return $self->{ "_gene_status" };
} # gene_status
=head2 clinical_symptoms
Title : clinical_symptoms
Usage : $omim->clinical_symptoms({});
Function: Set/get for the clinical symptoms of this OMIM entry.
Returns : [hash reference].
Args : [hash reference]. Suggested not to assign alone. Parser will do.
=cut
sub clinical_symptoms {
my ( $self, $value ) = @_;
if ( defined $value ) {
unless(ref($value) eq 'HASH'){
$self->throw('a hash referenced needed');
}
$self->{ "_clinical_symptoms" } = $value;
}
return $self->{ "_clinical_symptoms" };
} # clinical_symptoms
=head2 clinical_symptoms_raw
Title : clinical_symptoms_raw
Usage : $omim->clinical_symptoms( "Patients with ..." );
print $omim->clinical_symptoms();
Functions : Get/set for text information of clinical symptoms
Returns : The clinical symptoms [scalar].
Args : The clinical symptoms [scalar] (optional).
=cut
sub clinical_symptoms_raw {
my $self = shift;
return $self->{_clinical_symptoms_raw} = shift if @_;
return $self->{_clinical_symptoms_raw};
}
=head2 add_clinical_symptoms
Title : add_clinical_symptoms
Usage : $entry->add_clinical_symptoms('Ears', 'Floppy ears', 'Lop-ears');
Function : add one or more symptoms on one part of body.
Returns : [none]
Args : ($part, @symptoms)
$part, the text name of part/organism of human
@symptoms, an array of text description
=cut
sub add_clinical_symptoms {
my ($self, $part, @symptoms) = @_;
unless(defined $part){
$self->throw('a part/organism must be assigned');
}
$self->{_clinical_symptoms} = {} unless $self->{_clinical_symptoms};
$self->{_clinical_symptoms}->{$part} = []
unless $self->{_clinical_symptoms}->{$part};
push @{$self->{_clinical_symptoms}->{$part}}, @symptoms;
}
=head2 query_clinical_symptoms
Title : get_clinical_symptoms
Usage : @symptoms = $self->query_clinical_symptoms('Ears');
Function : get all symptoms specific to one part/organism.
Returns : an array of text
Args : $organ
=cut
sub query_clinical_symptoms {
my ($self, $organ)=@_;
my $symptoms=$self->{_clinical_symptoms}->{$organ};
@$symptoms;
}
sub get_clinical_symptom_organs {
my ($self)=@_;
keys %{$self->{_clinical_symptoms}};
}
=head2 created
Title : created
Usage : $omim->created( "Victor A. McKusick: 6/4/1986" );
or
print $omim->created();
Function: Set/get for the created field of the OMIM database.
Returns : Name(s) and date(s) [scalar - free form].
Args : Name(s) and date(s) [scalar - free form] (optional).
=cut
sub created {
my $self = shift;
return $self->{ "_created" } = shift if(@_);
return $self->{ "_created" };
} # created
=head2 contributors
Title : contributors
Usage : $omim->contributors( "Kelly A. Przylepa - revised: 03/18/2002" );
or
print $omim->contributors();
Function: Set/get for the contributors field of the OMIM database.
Returns : Name(s) and date(s) [scalar - free form].
Args : Name(s) and date(s) [scalar - free form] (optional).
=cut
sub contributors {
my $self = shift;
$self->{ "_contributors" } = shift if(@_);
return $self->{ "_contributors" };
} # contributors
=head2 edited
Title : edited
Usage : $omim->edited( "alopez: 06/03/1997" );
or
print $omim->edited();
Function: Set/get for the edited field of the OMIM database.
Returns : Name(s) and date(s) [scalar - free form].
Args : Name(s) and date(s) [scalar - free form] (optional).
=cut
sub edited {
my $self = shift;
return $self->{ "_edited" } = shift if(@_);
return $self->{ "_edited" };
} # edited
=head2 additional_references
Title : additional_references
Usage : $omim->additional_references( "Miller er al." );
or
print $omim->additional_references();
Function: Set/get for the additional references of this OMIM antry
(see also).
Returns : additional reference [scalar].
Args : additional reference [scalar] (optional).
=cut
sub additional_references {
my $self = shift;
return $self->{ "_additional_references" } = shift if(@_);
return $self->{ "_additional_references" };
} # additional_references
=head2 miniMIM
Title : miniMIM
Usage : $omim->miniMIM( $MM );
or
$MM = $omim->miniMIM();
Function: Set/get for the Mini MIM associated with this OMIM antry
(see also).
Returns : [Bio::Phenotype::OMIM::MiniMIMentry].
Args : [Bio::Phenotype::OMIM::MiniMIMentry] (optional).
=cut
sub miniMIM {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_check_ref_type( $value, "Bio::Phenotype::OMIM::MiniMIMentry" );
$self->{ "_mini_mim" } = $value;
}
return $self->{ "_mini_mim" };
}
=head2 each_AllelicVariant
Title : each_AllelicVariant()
Usage : @avs = $obj->each_AllelicVariant();
Function: Returns a list of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects
associated with this OMIM entry.
Returns : A list of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects.
Args :
=cut
sub each_AllelicVariant {
my ( $self ) = @_;
return @{$self->{"_allelic_variants"}} if exists($self->{"_allelic_variants"});
return ();
} # each_AllelicVariant
=head2 add_AllelicVariants
Title : add_AllelicVariants
Usage : $obj->add_AllelicVariants( @avs );
or
$obj->add_AllelicVariants( $av );
Function: Pushes one or more OMIMentryAllelicVariant
into the list of OMIMentryAllelicVariants.
Returns :
Args : Bio::Phenotype::OMIM::OMIMentryAllelicVariant object(s).
=cut
sub add_AllelicVariants {
my ( $self, @values ) = @_;
return unless( @values );
foreach my $value ( @values ) {
$self->_check_ref_type( $value, "Bio::Phenotype::OMIM::OMIMentryAllelicVariant" );
}
push( @{ $self->{ "_allelic_variants" } }, @values );
} # add_AllelicVariants
=head2 remove_AllelicVariants
Title : remove_AllelicVariants
Usage : $obj->remove_AllelicVariants();
Function: Deletes (and returns) the list of OMIMentryAllelicVariant objects
associated with this OMIM entry.
Returns : A list of OMIMentryAllelicVariant objects.
Args :
=cut
sub remove_AllelicVariants {
my ( $self ) = @_;
my @a = $self->each_AllelicVariant();
$self->{ "_allelic_variants" } = [];
return @a;
} # remove_AllelicVariants
# Title : _array_to_string
# Function:
# Returns :
# Args :
sub _array_to_string {
my( $self, @value ) = @_;
my $s = "";
for ( my $i = 0; $i < scalar( @value ); ++$i ) {
if ( ! ref( $value[ $i ] ) ) {
$s .= "#" . $i . "\n-- Value:\n" . $value[ $i ] . "\n";
}
elsif ( $value[ $i ]->isa( "Bio::Phenotype::OMIM::OMIMentryAllelicVariant" )
|| $value[ $i ]->isa( "Bio::Phenotype::Correlate" ) ) {
$s .= "#" . $i . "\n" . ( $value[ $i ] )->to_string() . "\n";
}
elsif ( $value[ $i ]->isa( "Bio::Annotation::Reference" ) ) {
$s .= "#".$i."\n-- Authors:\n".( $value[ $i ] )->authors()."\n";
$s .= "-- Title:\n".( $value[ $i ] )->title()."\n";
$s .= "-- Location:\n".( $value[ $i ] )->location()."\n";
}
elsif ( $value[ $i ]->isa( "Bio::Map::CytoPosition" ) ) {
$s .= "#" . $i . "\n-- Value:\n" . ( $value[ $i ] )->value() . "\n";
}
}
return $s;
} # _array_to_string
# Title :_is_true_or_false
# Function: Checks whether the argument is 1 or 0.
# Returns :
# Args : The value to be checked.
sub _is_true_or_false {
my ( $self, $value ) = @_;
unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
$self->throw( "Found [" . $value
. "] where " . TRUE . " or " . FALSE . " expected" );
}
} # _is_true_or_false
1;