Summary

simpleGOparser - a simple GO parser returning a SimpleGOEngine

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  use Bio::Ontology::simpleGOparser;

  my $parser = Bio::Ontology::simpleGOparser->new
	( -go_defs_file_name    => "/home/czmasek/GO/GO.defs",
	  -components_file_name => "/home/czmasek/GO/component.ontology",
	  -functions_file_name  => "/home/czmasek/GO/function.ontology",
	  -processes_file_name  => "/home/czmasek/GO/process.ontology" );

  my $engine = $parser->parse();

  my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
  my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );

Description

Needs Graph.pm from CPAN.

Methods

Methods description

 Title   : new
 Usage   : $parser = Bio::OntologyIO::simpleGOparser->new( -go_defs_file_name    => "/path/to/GO.defs",
                                                         -components_file_name => "/path/to/component.ontology"
                                                         -functions_file_name  => "/path/to/function.ontology"
                                                         -processes_file_name  => "/path/to/process.ontology" );                      
 Function: Creates a new simpleGOparser.
 Returns : A new simpleGOparser object.
 Args    : -go_defs_file_name    => the GO defs-file name
           -components_file_name => the component.ontology-file name
           -functions_file_name  => the function.ontology-file name
           -processes_file_name  => the process.ontology-file name

 Title   : init()
 Usage   : $parser->init();   
 Function: Initializes this object.
 Returns : 
 Args    :

 Title   : parse()
 Usage   : $parser->parse();   
 Function: Parses the files set wirh "new" or with methods
           go_defs_file_name, components_file_name, functions_file_name,
           processes_file_name.
 Returns : [Bio::Ontology::SimpleGOEngine]
 Args    :

 Title   : go_defs_file_name
 Usage   : $parser->go_defs_file_name( "GO.defs" );
 Function: Set/get for the GO defs-file_name.
 Returns : The GO defs-file_name [string].
 Args    : The GO defs-file_name [string] (optional).

 Title   : components_file_name
 Usage   : $parser-> components_file_name( "function.ontology" );
 Function: Set/get for the function ontology file name.
 Returns : The function ontology file name [string].
 Args    : The function ontology file name [string] (optional).

 Title   : functions_file_name
 Usage   : $parser->functions_file_name( "function.ontology" );
 Function: Set/get for functions file name.
 Returns : The functions file name [string].
 Args    : The functions file name [string] (optional).

 Title   : processes_file_name
 Usage   : $parser->processes_file_name( "GO.defs" );
 Function: Set/get for the processes file name.
 Returns : The processes file name [string].
 Args    : The processes file name [string] (optional).

Methods code

sub new {

    my( $class, @args ) = @_;
    
    my $self = $class->SUPER::new( @args );

    my ( $go_defs_file_name,
         $components,
         $functions,
         $processes, ) 
    = $self->_rearrange( [ qw( GO_DEFS_FILE_NAME
                               COMPONENTS_FILE_NAME
                               FUNCTIONS_FILE_NAME
                               PROCESSES_FILE_NAME ) ], @args );

    $self->init(); 
    
    $go_defs_file_name && $self->go_defs_file_name( $go_defs_file_name );
    $components        && $self->components_file_name( $components );
    $functions         && $self->functions_file_name( $functions );
    $processes         && $self->processes_file_name( $processes );
    
    
                         
    return $self;
} # new

}

sub init {

    my ( $self ) = @_;
    
    $self->{ "_go_defs_file_name" }    = undef;
    $self->{ "_components_file_name" } = undef;
    $self->{ "_functions_file_name" }  = undef;
    $self->{ "_processes_file_name" }  = undef;
    $self->_done( FALSE );
    $self->_not_first_record( FALSE );
    $self->_term( "" );
    
    $self->_go_engine( Bio::Ontology::SimpleGOEngine->new() );

} # init

}

sub parse {

    my ( $self ) = @_;
    my $x = 0;
    
    while( my $goterm = $self->_next_term() ) {
        $self->_add_term( $goterm );
    }

    if ( $self->components_file_name() ) {
        $self->_parse_relationships_file( $self->components_file_name(), "components ontology" );
    }
    if ( $self->functions_file_name() ) {
        $self->_parse_relationships_file( $self->functions_file_name(), "functions ontology" );
    }
    if ( $self->processes_file_name() ) {
        $self->_parse_relationships_file( $self->processes_file_name(), "processes ontology" );
    }
    
    return $self->_go_engine();
    
} # parse

}

sub go_defs_file_name {

    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_go_defs_file_name" } = $value;
        if ( $value =~ /\W/ ) {
            $self->_go_defs_file( new Bio::Root::IO->new( -file => $value ) );
        } 
    }
    
    return $self->{ "_go_defs_file_name" };
} # go_defs_file_name

}

sub components_file_name {

    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_components_file_name" } = $value;
    }
    
    return $self->{ "_components_file_name" };
} # components_file_name

}

sub functions_file_name {

    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_functions_file_name" } = $value;
    }
    
    return $self->{ "_functions_file_name" };
} # functions_file_name

}

sub processes_file_name {

    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_processes_file_name" } = $value;
    }
    
    return $self->{ "_processes_file_name" };
} # processes_file_name

}

sub _add_term {

    my ( $self, $term ) = @_;

    $self->_go_engine()->add_term( $term );


} # _add_term 

}

sub _part_of_relationship {

    my ( $self, $term ) = @_;

    return $self->_go_engine()->part_of_relationship();


} # _part_of_relationship 

}

sub _is_a_relationship {

    my ( $self, $term ) = @_;

    return $self->_go_engine()->is_a_relationship();


} # _is_a_relationship 

}

sub _add_relationship {

    my ( $self, $parent, $child, $type ) = @_;

   
    $self->_go_engine()->add_relationship( $parent, $child, $type );


} # _add_term 

}

sub _has_term {

    my ( $self, $term ) = @_;

    
    return $self->_go_engine()->has_term( $term );


} # _add_term

}

sub _parse_relationships_file {

    my ( $self, $file_name, $category ) = @_;
    
    my $file = new Bio::Root::IO->new( -file => $file_name );
    my $cat = Bio::Ontology::Term->new( -name => $category );
    
    my @stack       = ();
    my $prev_spaces = -1;
    my $prev_term   = "";
    
    
    while( my $line = $file->_readline() ) {
        
        if ( $line =~ /^!/ ) {
            next;
        }
        
        my $current_term   = $self->_get_first_goid( $line );
        my @isa_parents    = $self->_get_isa_goids( $line );
        my @partof_parents = $self->_get_partof_goids( $line );
        my @syns           = $self->_get_synonyms( $line );
        my @sec_go_ids     = $self->_get_secondary_goids( $line );
        my @cross_refs     = $self->_get_db_cross_refs( $line );
        
        
        if ( ! $self->_has_term( $current_term ) ) {
            my $goterm = $self->_create_GOentry( $self->_get_name( $line, $current_term ), $current_term );
            $self->_add_term( $goterm );
        }
        
        my $current_term_object = $self->_go_engine()->get_term( $current_term );
        
        $current_term_object->add_dblinks( @cross_refs );
        $current_term_object->add_secondary_GO_ids( @sec_go_ids );
        $current_term_object->add_synonyms( @syns );
        unless ( $line =~ /^\$/ ) {
            $current_term_object->category( $cat );
        }
        foreach my $parent ( @isa_parents ) {
            if ( ! $self->_has_term( $parent ) ) {
                my $goterm = $self->_create_GOentry( $self->_get_name( $line, $parent ), $parent );
                $self->_add_term( $goterm );
            }
            
            $self->_add_relationship( $parent,
                                      $current_term,
                                      $self->_is_a_relationship() );
             
        }
        foreach my $parent ( @partof_parents ) {
            if ( ! $self->_has_term( $parent ) ) {
                my $goterm = $self->_create_GOentry( $self->_get_name( $line, $parent ), $parent );
                $self->_add_term( $goterm );
            }
           
            $self->_add_relationship( $parent,
                                      $current_term,
                                      $self->_part_of_relationship() );
        }
        
        my $current_spaces = $self->_count_spaces( $line );
        
        if ( $current_spaces != $prev_spaces  ) {
       
            if ( $current_spaces == $prev_spaces + 1 ) {
                push( @stack, $prev_term ); 
            }
            elsif ( $current_spaces < $prev_spaces ) {
                my $n = $prev_spaces -  $current_spaces;
                for ( my $i = 0; $i < $n; ++$i ) {
                    pop( @stack );
                }
            }
            else {
                die( "format error" );
            } 
        }
        
        my $parent = $stack[ @stack - 1 ];
        
        
        if ( $line =~ /^\$/ ) {
        }
        elsif ( $line =~ /^\s*</ ) {
            $self->_add_relationship( $parent,
                                      $current_term,
                                      $self->_part_of_relationship() );
        }
        elsif ( $line =~ /^\s*%/ ) {
            $self->_add_relationship( $parent,
                                      $current_term,
                                      $self->_is_a_relationship() );
        }
        else {
            die( "format error" );
        }
        
        
        $prev_spaces = $current_spaces;
        
        $prev_term = $current_term;
        
    } 
} # _parse_relationships_file

}

sub _get_first_goid {

    my ( $self, $line ) = @_;
    
    if ( $line =~ /;\s*(GO:\d{7})/ ) {
        return $1;
    }
    else {
        die( "format error" );
    }
    
} # _get_first_goid

}

sub _get_name {

    my ( $self, $line, $goid ) = @_;
    
    if ( $line =~ /([^;^<^%^,]+);\s*$goid/ ) {
        my $name = $1;
        $name =~ s/\s+$//;
        $name =~ s/^\s+//;
        return $name;
    }
    else {
        return undef;
    }
} # _get_name   

}

sub _get_synonyms {

    my ( $self, $line ) = @_;
   
    my @synonyms = ();
   
    while ( $line =~ /synonym\s*:\s*([^;^<^%]+)/g ) {
        my $syn = $1;
        $syn =~ s/\s+$//;
        $syn =~ s/^\s+//;
        push( @synonyms, $syn );
    }
    return @synonyms;
    
} # _get_synonyms

}

sub _get_db_cross_refs {

    my ( $self, $line ) = @_;
   
    my @refs = ();
   
    while ( $line =~ /;([^;^<^%^:]+:[^;^<^%^:]+)/g ) {
        my $ref = $1;
        if ( $ref =~ /synonym/ || $ref =~ /GO:\d{7}/ ) {
            next;
        }
        $ref =~ s/\s+$//;
        $ref =~ s/^\s+//;
        push( @refs, $ref );
    }
    return @refs;

}

sub _get_secondary_goids {

    my ( $self, $line ) = @_;
    my @secs = ();
   
    while ( $line =~ /,\s*(GO:\d{7})/g ) {
        my $sec = $1;
        push( @secs, $sec );
    }
    return @secs;
    
} # _get_secondary_goids 

}

sub _get_isa_goids {

    my ( $self, $line ) = @_;
    
    my @ids = ();
    
    $line =~ s/GO:\d{7}//;
    
    while ( $line =~ /%[^<^,]*?(GO:\d{7})/g ) {
        push( @ids, $1 );
    }
    return @ids; 
} # _get_isa_goids

}

sub _get_partof_goids {

    my ( $self, $line ) = @_;
    
    my @ids = ();
    
    $line =~ s/GO:\d{7}//;
    
    while ( $line =~ /<[^%^,]*?(GO:\d{7})/g ) {
        push( @ids, $1 );
    }
    return @ids; 
    
    
} # _get_partof_goids

}

sub _count_spaces {

    my ( $self, $line ) = @_;
     
    if ( $line =~ /^([ ]+)/ ) {
         return length( $1 );
    }
    else {
         return 0;
    }
} # _count_spaces

}

sub _next_term {

    my ( $self ) = @_;

    if ( $self->_done() == TRUE ) {
        return undef;
    }
    
    my $line      = "";
    my $goid      = "";
    my $next_term = "";
    my $def       = "";
    my $comment   = "";
    my @def_refs  = ();
    
    while( $line = ( $self->_go_defs_file )->_readline() ) {
    
        if ( $line !~ /\S/ 
        ||   $line =~ /^\s*!/ ) {
            next;
        }
        
        elsif ( $line =~ /^\s*term:\s*(.+)/ ) {
            $next_term = $1;
            if ( $self->_not_first_record() == TRUE ) {
                my $entry = $self->_create_GOentry( $self->_term(), $goid, $def, $comment,\@ def_refs );
                $self->_term( $next_term );
                return $entry;
            }
            else {
                $self->_term( $next_term );
                $self->_not_first_record( TRUE );
            }
        }
        elsif ( $line =~ /^\s*goid:\s*(.+)/ ) {
            $goid = $1;
        }
        elsif ( $line =~ /^\s*definition:\s*(.+)/ ) {
            $def = $1;   
        }
        elsif ( $line =~ /^\s*definition_reference:\s*(.+)/ ) {
            push( @def_refs, $1 );  
        }
        elsif ( $line =~ /^\s*comment:\s*(.+)/ ) {
            $comment = $1;  
        }
    }
    $self->_done( TRUE );
    return $self->_create_GOentry( $self->_term(), $goid, $def, $comment,\@ def_refs );
} # _next_term

}

sub _go_engine {

    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_go_engine" } = $value;
    }
    
    return $self->{ "_go_engine" };
} # _go_enginee

}

sub _create_GOentry {

    my ( $self, $name, $goid ) = @_;

    my $term = Bio::Ontology::GOterm->new();

    $term->GO_id( $goid );
    $term->name( $name );
    
    return $term;

} # _create_GOentry

}

sub _not_first_record {

    my ( $self, $value ) = @_;

    if ( defined $value ) {
        unless ( $value == FALSE || $value == TRUE ) {
            $self->throw( "Argument to method\" _not_first_record\" must be either ".TRUE." or ".FALSE );
        }
        $self->{ "_not_first_record" } = $value;
    }
    
    return $self->{ "_not_first_record" };
} # _not_first_record

}

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

}

sub _go_defs_file {

    my ( $self, $value ) = @_;

    if ( defined $value ) {
        unless ( $value->isa( "Bio::Root::IO" ) ) {
            $self->throw( "Argument to method\" _go_defs_File\" is not a valid\" Bio::Root::IO\"" );
        }
        $self->{ "_go_defs_file" } = $value;
     
    }
    
    return $self->{ "_go_defs_file" };
} # _go_defs_file

}

sub _term {

    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_term" } = $value;
    }
    
    return $self->{ "_term" };
} # _term  

}

General documentation

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
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report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Christian M. Zmasek
Email: czmasek@gnf.org or cmzmasek@hotmail.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:

  Genomics Institute of the Novartis Research Foundation
  10675 John Jay Hopkins Drive
  San Diego, CA 92121

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _