Bio::Phenotype::OMIM OMIMparser
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Summary
Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database
Package variables
No package variables defined.
Included modules
Bio::Annotation::Reference
Bio::Map::CytoPosition
Bio::Phenotype::Correlate
Bio::Phenotype::OMIM::OMIMentry
Bio::Phenotype::OMIM::OMIMentryAllelicVariant
Bio::Root::IO
Bio::Species
Inherit
Bio::Root::Root
Synopsis
  use Bio::Phenotype::OMIM::OMIMparser;
# The OMIM database is available as textfile at: # ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z
# The genemap is available as textfile at:
# ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap
$omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap => "/path/to/genemap", -omimtext => "/path/to/omim.txt" ); while ( my $omim_entry = $omim_parser->next_phenotype() ) { # This prints everything. print( $omim_entry->to_string() ); print "\n\n"; # This gets individual data (some of them object-arrays) # (and illustrates the relevant methods of OMIMentry). my $numb = $omim_entry->MIM_number(); # *FIELD* NO my $title = $omim_entry->title(); # *FIELD* TI - first line my $alt = $omim_entry->alternative_titles_and_symbols(); # *FIELD* TI - additional lines my $mtt = $omim_entry->more_than_two_genes(); # "#" before title my $sep = $omim_entry->is_separate(); # "*" before title my $desc = $omim_entry->description(); # *FIELD* TX my $mm = $omim_entry->mapping_method(); # from genemap my $gs = $omim_entry->gene_status(); # from genemap my $cr = $omim_entry->created(); # *FIELD* CD my $cont = $omim_entry->contributors(); # *FIELD* CN my $ed = $omim_entry->edited(); # *FIELD* ED my $sa = $omim_entry->additional_references(); # *FIELD* SA my $cs = $omim_entry->clinical_symptoms_raw(); # *FIELD* CS my $comm = $omim_entry->comment(); # from genemap my $mini_mim = $omim_entry->miniMIM(); # *FIELD* MN # A Bio::Phenotype::OMIM::MiniMIMentry object. # class Bio::Phenotype::OMIM::MiniMIMentry # provides the following: # - description() # - created() # - contributors() # - edited() # # Prints the contents of the MINI MIM entry (most OMIM entries do # not have MINI MIM entries, though). print $mini_mim->description()."\n"; print $mini_mim->created()."\n"; print $mini_mim->contributors()."\n"; print $mini_mim->edited()."\n"; my @corrs = $omim_entry->each_Correlate(); # from genemap # Array of Bio::Phenotype::Correlate objects. # class Bio::Phenotype::Correlate # provides the following: # - name() # - description() (not used) # - species() (always mouse) # - type() ("OMIM mouse correlate") # - comment() my @refs = $omim_entry->each_Reference(); # *FIELD* RF # Array of Bio::Annotation::Reference objects. my @avs = $omim_entry->each_AllelicVariant(); # *FIELD* AV # Array of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects. # class Bio::Phenotype::OMIM::OMIMentryAllelicVariant # provides the following: # - number (e.g ".0001" ) # - title (e.g "ALCOHOL INTOLERANCE" ) # - symbol (e.g "ALDH2*2" ) # - description (e.g "The ALDH2*2-encoded protein has a change ..." ) # - aa_ori (used if information in the form "LYS123ARG" is found) # - aa_mut (used if information in the form "LYS123ARG" is found) # - position (used if information in the form "LYS123ARG" is found) # - additional_mutations (used for e.g. "1-BP DEL, 911T") my @cps = $omim_entry->each_CytoPosition(); # from genemap # Array of Bio::Map::CytoPosition objects. my @gss = $omim_entry->each_gene_symbol(); # from genemap # Array of strings. # do something ... }
Description
This parser returns Bio::Phenotype::OMIM::OMIMentry objects
(which inherit from Bio::Phenotype::PhenotypeI).
It parses the OMIM database available as
ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z
together with (optionally) the gene map file at
ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap.
Methods
newDescriptionCode
next_phenotypeDescriptionCode
initDescriptionCode
genemap_file_nameDescriptionCode
omimtxt_file_nameDescriptionCode
_createOMIMentry
No description
Code
_finer_parse_symptoms
No description
Code
_parse_genemap
No description
Code
_parse_allelic_variants
No description
Code
_create_allelic_variant
No description
Code
_parse_title
No description
Code
_parse_references
No description
Code
_genemap_hash
No description
Code
_is_not_first_record
No description
Code
_done
No description
Code
_OMIM_text_file
No description
Code
_read_genemap
No description
Code
_no_OMIM_text_file_provided_error
No description
Code
_not_a_OMIM_text_file_error
No description
Code
_add_to_hash
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap => "/path/to/genemap",
-omimtext => "/path/to/omim.txt" );
Function: Creates a new OMIMparser.
Returns : A new OMIMparser object.
Args : -genemap => the genemap file name (optional)
-omimtext => the omim text file name
next_phenotypecodeprevnextTop
 Title   : next_phenotype()
Usage : while ( my $omim_entry = $omim_parser->next_phenotype() ) {
# do something with $omim_entry
}
Function: Returns an Bio::Phenotype::OMIM::OMIMentry or
undef once the end of the omim text file is reached.
Returns : A Bio::Phenotype::OMIM::OMIMentry.
Args :
initcodeprevnextTop
 Title   : init()
Usage : $omim_parser->init();
Function: Initializes this OMIMparser to all "".
Returns :
Args :
genemap_file_namecodeprevnextTop
 Title   : genemap_file_name
Usage : $omimparser->genemap_file_name( "genemap" );
Function: Set/get for the genemap file name.
Returns : The genemap file name [string].
Args : The genemap file name [string] (optional).
omimtxt_file_namecodeprevnextTop
 Title   : omimtxt_file_name
Usage : $omimparser->omimtxt_file_name( "omim.txt" );
Function: Set/get for the omim text file name.
Returns : The the omim text file name [string].
Args : The the omim text file name [string] (optional).
Methods code
newdescriptionprevnextTop
sub new {
    my( $class, @args ) = @_;
    
    my $self = $class->SUPER::new( @args );

    my ( $genemap_file_name, $omimtxt_file_name ) 
    = $self->_rearrange( [ qw( GENEMAP OMIMTEXT ) ], @args );

    $self->init(); 
    
    $genemap_file_name && $self->genemap_file_name( $genemap_file_name );
    
    $omimtxt_file_name && $self->omimtxt_file_name( $omimtxt_file_name);
                         
    return $self;
}
next_phenotypedescriptionprevnextTop
sub next_phenotype {
    my ( $self ) = @_;
    
    unless( defined( $self->_OMIM_text_file() ) ) {
        $self->_no_OMIM_text_file_provided_error();
    }
    
    if ( $self->_done() == TRUE ) {
        return;
    }

    my $fieldtag          = "";
    my $contents          = "";
    my $line              = "";
    my $state             = DEFAULT_STATE;
    my $saw_mini_min_flag = FALSE;
    my %record            = ();
    
    while( $line = ( $self->_OMIM_text_file )->_readline() ) {
        if ( $line =~ /^\s*\*RECORD\*/ ) {
            if ( $self->_is_not_first_record() == TRUE ) {
                $self->_add_to_hash( $state, $contents,\%record );
                my $omim_entry = $self->_createOMIMentry(\% record );
                return $omim_entry;
            }
            else {
                $self->_is_not_first_record( TRUE );
            }
            
        }
        elsif ( $line =~ /^\s*\*FIELD\*\s*(\S+)/ ) {
            $fieldtag = $1;
            if ( $state != DEFAULT_STATE ) {
                $self->_add_to_hash( $state, $contents,\%record );
            }
            $contents = "";
            
            if ( $fieldtag eq "NO" ) {
                $state = MIM_NUMBER_STATE;
                $saw_mini_min_flag = FALSE;   
            }
            elsif ( $fieldtag eq "TI" ) {
                $state = TITLE_STATE;
                $saw_mini_min_flag = FALSE;   
            }
            elsif ( $fieldtag eq "TX" ) {
                $state = TEXT_STATE;
                $saw_mini_min_flag = FALSE;   
            }
            elsif ( $fieldtag eq "MN" ) {
                $state = MINI_MIM_TEXT_STATE;
                $saw_mini_min_flag = TRUE;           
            }
            elsif ( $fieldtag eq "AV" ) {
                $state = ALLELIC_VARIANT_STATE;
                $saw_mini_min_flag = FALSE;     
            }
            elsif ( $fieldtag eq "SA" ) { 
                $state = SEE_ALSO_STATE;
                $saw_mini_min_flag = FALSE;   
            }
            elsif ( $fieldtag eq "RF" ) {
                $state = REF_STATE;
                $saw_mini_min_flag = FALSE;   
            }
            elsif ( $fieldtag eq "CS" ) {
                $state = SYMPT_STATE;
                $saw_mini_min_flag = FALSE;   
            }
            elsif ( $fieldtag eq "CN" ) {
                if ( $saw_mini_min_flag == TRUE ) {
                    $state = MINI_MIM_CONTRIBUTORS_STATE;
                }
                else {
                    $state = CONTRIBUTORS_STATE;
                }     
            }
            elsif ( $fieldtag eq "CD" ) {
                if ( $saw_mini_min_flag == TRUE ) {
                    $state = MINI_MIM_CREATED_BY_STATE;
                }
                else {
                    $state = CREATED_BY_STATE;
                }     
            }
            elsif ( $fieldtag eq "ED" ) {
                if ( $saw_mini_min_flag == TRUE ) {
                    $state = MINI_MIM_EDITED_BY_STATE;
                }
                else {
                    $state = EDITED_BY_STATE;
                }     
            }
            else {
                print "Warning: Unknown tag: $fieldtag\n";
            }

        }
        else {
            $contents .= $line;
        }
    }

    $self->_OMIM_text_file()->close();
    $self->_done( TRUE );

    unless( %record ) {
        $self->_not_a_OMIM_text_file_error();
    }

    $self->_add_to_hash( $state, $contents,\%record );
    
    my $omim_entry = $self->_createOMIMentry(\% record );
    
    return $omim_entry;

} # next_phenotype
}
initdescriptionprevnextTop
sub init {
    my ( $self ) = @_;
    
    $self->genemap_file_name( "" );
    $self->omimtxt_file_name( "" );
    $self->_genemap_hash( {} );
    $self->_OMIM_text_file( undef );
    $self->_is_not_first_record( FALSE );
    $self->_done( FALSE );

} # init
}
genemap_file_namedescriptionprevnextTop
sub genemap_file_name {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_genemap_file_name" } = $value;
        $self->_genemap_hash( $self->_read_genemap( $value ) );
    }
    
    return $self->{ "_genemap_file_name" };
} # genemap_file_name
}
omimtxt_file_namedescriptionprevnextTop
sub omimtxt_file_name {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_omimtxt_file_name" } = $value;
        if ( $value =~ /\W/ ) {
            $self->_OMIM_text_file( Bio::Root::IO->new->new( -file => $value ) );
        } 
    }
    
    return $self->{ "_omimtxt_file_name" };
} # omimtxt_file_name
}
_createOMIMentrydescriptionprevnextTop
sub _createOMIMentry {
    my ( $self, $record_ref ) = @_;
    
    my $omim_entry = Bio::Phenotype::OMIM::OMIMentry->new();
    my $mini_mim   = Bio::Phenotype::OMIM::MiniMIMentry->new();
    
    while ( ( my $key, my $val ) = each( %$record_ref ) ) {
        
        $val =~ s/^\s+//;
        $val =~ s/\s+$//;
        
        if ( $key == MIM_NUMBER_STATE ) {
            $val =~ s/\s+//g;
            $val =~ s/\D//g;
           
            $omim_entry->MIM_number( $val );
            
            my $gm = $self->_genemap_hash();
            if ( exists( $$gm{ $val } ) ) {
                $self->_parse_genemap( $omim_entry, $val );
            }
            
        }
        elsif ( $key == TITLE_STATE ) {
            my ( $title, $alt_titles ) = $self->_parse_title( $val );
            $omim_entry->title( $title );
            $omim_entry->alternative_titles_and_symbols( $alt_titles );
            if ( $title =~ /^\*/ ) {
                 $omim_entry->is_separate( TRUE );
            }
            elsif ( $title =~ /^#/ ) {
                 $omim_entry->more_than_two_genes( TRUE );
            } 
        }
        elsif ( $key == TEXT_STATE ) {
            $val = undef if($val =~ /DESCRIPTION1\nDESCRIPTION2/);
            $omim_entry->description( $val );
        }
        elsif ( $key == ALLELIC_VARIANT_STATE ) {
            my @allelic_variants =  $self->_parse_allelic_variants( $val );
            $omim_entry->add_AllelicVariants( @allelic_variants );
        }
        elsif ( $key == SEE_ALSO_STATE ) {
            $omim_entry->additional_references( $val );
        }
        elsif ( $key == REF_STATE ) {
            my @refs =  $self->_parse_references( $val );
            $omim_entry->add_References( @refs );
        }
        elsif ( $key == SYMPT_STATE ) {
            $val = '' if($val eq 'clinical symptoms');
            $omim_entry->clinical_symptoms_raw( $val );
        }
        elsif ( $key == CONTRIBUTORS_STATE ) {
            $val = undef if($val =~ /cn1\ncn2\ncn3/);
            $omim_entry->contributors( $val );
        }
        elsif ( $key == CREATED_BY_STATE ) {
            $val = undef if($val =~ /cd1\ncd2\ncd3/);
            $omim_entry->created( $val );
        }
        elsif ( $key == EDITED_BY_STATE ) {
            $val = undef if($val =~ /ed1\ned2\ned3/);
            $omim_entry->edited( $val );
        }
        elsif ( $key == MINI_MIM_TEXT_STATE ) {
            $mini_mim->description( $val );
        }
        elsif ( $key == MINI_MIM_CONTRIBUTORS_STATE ) {
            $mini_mim->contributors( $val );
        }
        elsif ( $key == MINI_MIM_CREATED_BY_STATE ) {
            $mini_mim->created( $val );
        }
        elsif ( $key == MINI_MIM_EDITED_BY_STATE ) {
            $mini_mim->edited( $val );
        }
    
    }
    
    my $man = Bio::Species->new();
    $man->classification( qw( sapiens Homo ) );
    $man->common_name( "man" );
    $omim_entry->species( $man );
    $omim_entry->miniMIM( $mini_mim );

    # parse the symptoms text into a hash-based structure.
$self->_finer_parse_symptoms($omim_entry); return $omim_entry; } # _createOMIMentry
}
_finer_parse_symptomsdescriptionprevnextTop
sub _finer_parse_symptoms {
    my ($self, $omim_entry) = @_;
    my $text = $omim_entry->clinical_symptoms_raw;
    if( $text ) { 
	my $part;
	for my $line (split /\n/, $text){
		if ($line =~ /^([\w\s,]+)\:\s*$/) {
		$part = $1;
	    } elsif( $line =~ /^\s+$/ ) {
	    } elsif($line =~ /^(\s+)([^;]+)\;?\s*$/){
		my $symptom = $2;
		if( ! $part ) { 
		    # $self->warn("$text\nline='$line'\n");
next; } $omim_entry->add_clinical_symptoms($part, $symptom); } } } $omim_entry->clinical_symptoms_raw('');
}
_parse_genemapdescriptionprevnextTop
sub _parse_genemap {
     my ( $self, $omim_entry, $val ) = @_;
     
     my $genemap_line = ${ $self->_genemap_hash() }{ $val };
     my @a = split( /\|/, $genemap_line );

     my $locations = $a[ 4 ];
     if ( defined ( $locations ) ) {
          $locations =~ s/\s+//g;
          my @ls = split( /[,;]/, $locations );
          my @cps;
          foreach my $l ( @ls ) {
               my $cp = Bio::Map::CytoPosition->new( -value => $l );
               push( @cps, $cp ); 
          }
          $omim_entry->add_CytoPositions( @cps );
      }

     my $gene_symbols = $a[ 5 ];
     if ( defined ( $gene_symbols ) ) {
          $gene_symbols =~ s/\s+//g;
          my @gss = split( /[,;]/, $gene_symbols );
          $omim_entry->add_gene_symbols( @gss );
     }

     my $mouse_correlates = $a[ 16 ];
     if ( defined ( $mouse_correlates ) ) {
          $mouse_correlates =~ s/\s+//g;
          my @mcs = split( /[,;]/, $mouse_correlates );
          my @cs;
          foreach my $mc ( @mcs ) {
               my $mouse = Bio::Species->new();
               $mouse->classification( qw( musculus Mus ) );
               $mouse->common_name( "mouse" );
               my $c = Bio::Phenotype::Correlate->new();
               $c->name( $mc );
               $c->species( $mouse );
               $c->type( "OMIM mouse correlate" );

               push( @cs, $c ); 
          }
          $omim_entry->add_Correlates( @cs );
     }

     $omim_entry->gene_status( $a[ 6 ] ) if defined $a[ 6 ];
     $omim_entry->mapping_method( $a[ 10 ] ) if defined $a[ 10 ];
     $omim_entry->comment( $a[ 11 ] ) if defined $a[ 11 ];

} # _parse_genemap
}
_parse_allelic_variantsdescriptionprevnextTop
sub _parse_allelic_variants {
    my ( $self, $text ) = @_;
    
    my @allelic_variants;
    my $number          = "";
    my $title           = "";
    my $symbol_mut_line = "";
    my $prev_line       = "";
    my $description     = "";
    my $saw_empty_line  = FALSE;
     
    my @lines = split( /\n/, $text );
    
    foreach my $line ( @lines ) {
        if ( $line !~ /\w/ ) {
             $saw_empty_line = TRUE;
        }
        elsif ( $line =~ /^\s*(\.\d+)/ ) {
            my $current_number = $1;
            if ( $number ne "" ) {
                my $allelic_variant = $self->_create_allelic_variant( $number, $title, 
                                                    $symbol_mut_line, $description );
                
                push( @allelic_variants, $allelic_variant );
            }
            $number          = $current_number;
            $title           = "";
            $prev_line       = "";
            $symbol_mut_line = "";
            $description     = "";
            $saw_empty_line  = FALSE;
        }
        elsif ( $title eq "" ) {
            $title = $line;
        }
        elsif ( $saw_empty_line == FALSE ) {
            $prev_line = $line;
        }
        elsif ( $saw_empty_line == TRUE ) {
            if ( $prev_line ne "" ) {
                $symbol_mut_line = $prev_line;
                $prev_line       = "";
            }
            if ( $description ne "" ) {
                $description .= "\n" . $line;
            }
            else {
                $description = $line;
            }
        }
    }
    
    my $allelic_variant = $self->_create_allelic_variant( $number, $title, 
                                        $symbol_mut_line, $description );
    
    push( @allelic_variants, $allelic_variant );
    
    return @allelic_variants;
    
} # _parse_allelic_variants
}
_create_allelic_variantdescriptionprevnextTop
sub _create_allelic_variant {
    my ( $self, $number, $title, $symbol_mut_line, $description ) = @_;
    
    my $symbol   = "";
    my $mutation = "";
    my $aa_ori   = "";
    my $aa_mut   = "";
    my $position = "";
   
    if ( $symbol_mut_line =~ /\s*(.+?)\s*,\s*([a-z]{3})(\d+)([a-z]{3})/i ) {
         $symbol   = $1;
         $aa_ori   = $2;
         $aa_mut   = $4;
         $position = $3;
    }
    elsif ( $symbol_mut_line =~ /\s*(.+?)\s*,\s*(.+)/ ) {
         $symbol   = $1;
         $mutation = $2;
    }
    else {
         $symbol = $symbol_mut_line;
    }
    
    if ( ! defined( $description ) ) { $self->throw("undef desc"); }
    if ( ! defined( $mutation ) )   { $self->throw("undef mutation"); }
  
    
    my $allelic_variant = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new();
    $allelic_variant->number( $number );
    $allelic_variant->aa_ori( $aa_ori );
    $allelic_variant->aa_mut( $aa_mut );
    $allelic_variant->position( $position );
    $allelic_variant->title( $title );
    $allelic_variant->symbol( $symbol );
    $allelic_variant->description( $description );
    $allelic_variant->additional_mutations( $mutation );
     
    return $allelic_variant; 
    
} # _create_allelic_variant
}
_parse_titledescriptionprevnextTop
sub _parse_title {
    my ( $self, $text ) = @_;
    my $title = "";
    if ( $text =~ /^(.+)\n/ ) {
        $title = $1;
        $text  =~ s/^.+\n//;
    }
    else {
        $title = $text;
        $text  = "";
    
    }
    
    return ( $title, $text ); 
} # _parse_title
}
_parse_referencesdescriptionprevnextTop
sub _parse_references {
    my ( $self, $text ) = @_;
    
    $text =~ s/\A\s+//;
    $text =~ s/\s+\z//;
    $text =~ s/\A\d+\.\s*//;
    
    my @references;
    
    my @texts = split( /\s*\n\s*\n\s*\d+\.\s*/, $text );
    
    foreach my $t ( @texts ) {
    
        my $authors   = "";
        my $title     = "";
        my $location  = "";
        
        $t =~ s/\s+/ /g;
        
        if ( $t =~ /(.+?)\s*:\s*(.+?[.?!])\s+(.+?)\s+(\S+?)\s*:\s*(\w?\d+.*)\s*,\s*(\d+)/ ) {
            $authors    = $1;
            $title      = $2;
            my $journal = $3;
            my $volume  = $4;
            my $fromto  = $5;
            my $year    = $6;
            my $from    = "",
            my $to      = "";
            if ( $fromto =~ /(\d+)-+(\d+)/ ) {
                $from = $1;
                $to   = "-".$2;
            }
            elsif ( $fromto =~ /\A(\w+)/ ) {
                $from = $1;
            }
            $location = $journal." ".$volume." ".$from.$to." (".$year.")";
        }
       
            
        elsif ( $t =~ /(.+?)\s*:\s*(.+?[.?!])\s*(.+?)\z/ ) {
            $authors   = $1;
            $title     = $2;
            $location  = $3;
        }
        else {
            $title = $t;  
        }
         
        my $ref = Bio::Annotation::Reference->new( -title    => $title,
                                                   -location => $location,
                                                   -authors  => $authors );
        push( @references, $ref );
       
    }
    return @references;
    
} # _parse_references
}
_genemap_hashdescriptionprevnextTop
sub _genemap_hash {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        unless ( ref( $value ) eq "HASH" ) {
            $self->throw( "Argument to method\" _genemap_hash\" is not a reference to an Hash" );
        }
        $self->{ "_genemap_hash" } = $value;
     
    }
    
    return $self->{ "_genemap_hash" };
} # _genemap_hash
}
_is_not_first_recorddescriptionprevnextTop
sub _is_not_first_record {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        unless ( $value == FALSE || $value == TRUE ) {
            $self->throw( "Found [$value] where [" . TRUE
            ." or " . FALSE . "] expected" );
        }
        $self->{ "_not_first_record" } = $value;
    }
    
    return $self->{ "_not_first_record" };
} # _is_not_first_record
}
_donedescriptionprevnextTop
sub _done {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        unless ( $value == FALSE || $value == TRUE ) {
            $self->throw( "Found [$value] where [" . TRUE
            ." or " . FALSE . "] expected" );
        }
        $self->{ "_done" } = $value;
    }
    
    return $self->{ "_done" };
} # _done
}
_OMIM_text_filedescriptionprevnextTop
sub _OMIM_text_file {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        unless ( $value->isa( "Bio::Root::IO" ) ) {
            $self->throw( "[$value] is not a valid\" Bio::Root::IO\"" );
        }
        $self->{ "_omimtxt_file" } = $value;
     
    }
    
    return $self->{ "_omimtxt_file" };
} # _OMIM_text_file
}
_read_genemapdescriptionprevnextTop
sub _read_genemap {
    my ( $self, $genemap_file_name ) = @_;
    
    my $line         = "";
    my %genemap_hash = ();
    my $genemap_file = Bio::Root::IO->new( -file => $genemap_file_name );
    my @a            = ();
    my %gm           = ();
    
    while( $line = $genemap_file->_readline() ) {
        @a = split( /\|/, $line );
        unless( scalar( @a ) == 18 ) {
            $self->throw( "Gene map file\" ".$self->genemap_file_name()
            . "\" is not in the expected format."
            . " Make sure there is a linebreak after the final line." );
        }
        $gm{ $a[ 9 ] } = $line;
    }
    $genemap_file->close();
    $self->_genemap_hash(\% gm );
  
} #_read_genemap 
}
_no_OMIM_text_file_provided_errordescriptionprevnextTop
sub _no_OMIM_text_file_provided_error {
    my ( $self ) = @_;

    my $msg =  "Need to indicate a OMIM text file to read from with\n";
    $msg .= "either\" OMIMparser->new( -omimtext =>\" path/to/omim.txt\" );\"\n";
    $msg .= "or\"\$ omim_parser->omimtxt_file_name(\" path/to/omim.txt\" );\"";
    $self->throw( $msg );
} # _no_OMIM_text_file_provided_error
}
_not_a_OMIM_text_file_errordescriptionprevnextTop
sub _not_a_OMIM_text_file_error {
    my ( $self ) = @_;

    my $msg =  "File\" ".$self->omimtxt_file_name() . 
    "\" appears not to be a OMIM text file";
    $self->throw( $msg );
} # _not_a_OMIM_text_file_error
}
_add_to_hashdescriptionprevnextTop
sub _add_to_hash {
    my ( $self, $state, $contents, $record_ref ) = @_;
    
    if ( exists( $record_ref->{ $state } ) ) {
        chomp( $record_ref->{ $state } );
        $record_ref->{ $state } = $record_ref->{ $state } . $contents;
    }
    else {
        $record_ref->{ $state } = $contents;
    }
} # _add_to_hash
1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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 BugsTop
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/
AUTHORTop
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
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _