Bio::Phenotype::OMIM
OMIMentry
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Summary
Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian
Inheritance in Man) database entries
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
$obj = Bio::Phenotype::OMIM::OMIMentry->new( -mim_number => 200000,
-description => "This is ...",
-more_than_two_genes => 1 );
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.
Methods
Methods description
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 |
Title : init()
Usage : $obj->init();
Function: Initializes this OMIMentry to all "" and empty lists.
Returns :
Args : |
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). |
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). |
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). |
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). |
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). |
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). |
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). |
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. |
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). |
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 |
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 |
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). |
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). |
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). |
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). |
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). |
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 : |
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). |
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 : |
Methods code
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;
}
} | 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() );
}
} | 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;
}
} | 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" };
}
} | sub title
{ my $self = shift;
$self->name(@_);
}
} | sub alternative_titles_and_symbols
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_alternative_titles_and_symbols" } = $value;
}
return $self->{ "_alternative_titles_and_symbols" };
}
} | 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" };
}
} | sub is_separate
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_is_true_or_false( $value );
$self->{ "_is_separate" } = $value;
}
return $self->{ "_is_separate" };
}
} | sub mapping_method
{ my $self = shift;
return $self->{ "_mapping_method" } = shift if(@_);
return $self->{ "_mapping_method" };
}
} | sub gene_status
{ my ( $self, $value ) = @_;
if ( defined $value ) {
unless ( $value eq "C"
|| $value eq "P"
|| $value eq "I"
|| $value eq "L"
|| $value eq "" ) {
$value = "";
}
$self->{ "_gene_status" } = $value;
}
return $self->{ "_gene_status" };
}
} | 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" };
}
} | sub clinical_symptoms_raw
{ my $self = shift;
return $self->{_clinical_symptoms_raw} = shift if @_;
return $self->{_clinical_symptoms_raw};} | sub add_clinical_symptoms
{ my ($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;} | 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}};} | sub created
{ my $self = shift;
return $self->{ "_created" } = shift if(@_);
return $self->{ "_created" };
}
} | sub contributors
{ my $self = shift;
$self->{ "_contributors" } = shift if(@_);
return $self->{ "_contributors" };
}
} | sub edited
{ my $self = shift;
return $self->{ "_edited" } = shift if(@_);
return $self->{ "_edited" };
}
} | sub additional_references
{ my $self = shift;
return $self->{ "_additional_references" } = shift if(@_);
return $self->{ "_additional_references" };
}
} | 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" };} | sub each_AllelicVariant
{ my ( $self ) = @_;
return @{$self->{"_allelic_variants"}} if exists($self->{"_allelic_variants"});
return ();
}
} | 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 );
}
} | sub remove_AllelicVariants
{ my ( $self ) = @_;
my @a = $self->each_AllelicVariant();
$self->{ "_allelic_variants" } = [];
return @a;
}
} | 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;
}
} | | _is_true_or_false | description | prev | next | Top |
sub _is_true_or_false
{ my ( $self, $value ) = @_;
unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
$self->throw( "Found [" . $value
. "] where " . TRUE . " or " . FALSE . " expected" );
}
}
1;} | General documentation
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Please direct usage questions or support issues to the mailing list:
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rather than to the module maintainer directly. Many experienced and
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with code and data examples if at all possible.
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/
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _