Bio::Phenotype::OMIM
OMIMparser
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Summary
OMIMparser - parser for the OMIM database
Package variables
No package variables defined.
Included modules
Inherit
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(); # *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
Methods
Methods description
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). |
Title : init()
Usage : $omim_parser->init();
Function: Initializes this OMIMparser to all "".
Returns :
Args : |
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 |
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 : |
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
| _OMIM_text_file | description | prev | next | Top |
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" };
}
} | 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;
}
}
1;} | 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 ) {
$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 ) {
$omim_entry->clinical_symptoms( $val );
}
elsif ( $key == CONTRIBUTORS_STATE ) {
$omim_entry->contributors( $val );
}
elsif ( $key == CREATED_BY_STATE ) {
$omim_entry->created( $val );
}
elsif ( $key == EDITED_BY_STATE ) {
$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 );
return $omim_entry;
}
} | 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 ) ) { die( "undef desc" ); }
if ( ! defined( $mutation ) ) { die( "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;
}
} | 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" };
}
} | 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" };
}
} | 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" };
}
} | | _no_OMIM_text_file_provided_error | description | prev | next | Top |
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 );
}
} | 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 );
}
} | 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;
}
} | 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 ];
}
} | 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;
}
} | sub _parse_title
{ my ( $self, $text ) = @_;
my $title = "";
if ( $text =~ /^(.+)\n/ ) {
$title = $1;
$text =~ s/^.+\n//;
}
else {
$title = $text;
$text = "";
}
return ( $title, $text );
}
} | sub _read_genemap
{ my ( $self, $genemap_file_name ) = @_;
my $line = "";
my %genemap_hash = ();
my $genemap_file = new 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" );
}
$gm{ $a[ 9 ] } = $line;
}
$genemap_file->close();
$self->_genemap_hash(\% gm );
}
} | sub genemap_file_name
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_genemap_file_name" } = $value;
if ( $value =~ /\W/ ) {
_genemap_hash( $self->_read_genemap( $value ) );
}
}
return $self->{ "_genemap_file_name" };
}
} | 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 );
}
} | 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;} | sub next_phenotype
{ my ( $self ) = @_;
unless( defined( $self->_OMIM_text_file() ) ) {
$self->_no_OMIM_text_file_provided_error();
}
if ( $self->_done() == TRUE ) {
return undef;
}
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;
}
} | sub omimtxt_file_name
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_omimtxt_file_name" } = $value;
if ( $value =~ /\W/ ) {
$self->_OMIM_text_file( new Bio::Root::IO->new( -file => $value ) );
}
}
return $self->{ "_omimtxt_file_name" };
}
} | General documentation
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the bugs and their resolution. Bug reports can be submitted via
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bioperl-bugs@bio.perl.org
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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _