#
# BioPerl module for Bio::OntologyIO::dagflat
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp, hlapp at gmx.net
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (c) Hilmar Lapp, hlapp at gmx.net, 2003.
# (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::OntologyIO::dagflat - a base class parser for GO flat-file type formats
=head1 SYNOPSIS
use Bio::OntologyIO;
# do not use directly -- use via Bio::OntologyIO
# e.g., the GO parser is a simple extension of this class
my $parser = Bio::OntologyIO->new
( -format => "go",
-defs_file => "/home/czmasek/GO/GO.defs",
-files => ["/home/czmasek/GO/component.ontology",
"/home/czmasek/GO/function.ontology",
"/home/czmasek/GO/process.ontology"] );
my $go_ontology = $parser->next_ontology();
my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
my $RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );
=head1 DESCRIPTION
Needs Graph.pm from CPAN.
=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
=head2 CONTRIBUTOR
Hilmar Lapp, hlapp at gmx.net
=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::OntologyIO::dagflat;
use strict;
use Bio::Root::IO;
use Bio::Ontology::OBOEngine;
use Bio::Ontology::Ontology;
use Bio::Ontology::OntologyStore;
use Bio::Ontology::TermFactory;
use Bio::Annotation::DBLink;
use constant TRUE => 1;
use constant FALSE => 0;
use base qw(Bio::OntologyIO);
=head2 new
Title : new
Usage : $parser = Bio::OntologyIO->new(
-format => "go",
-defs_file => "/path/to/GO.defs",
-files => ["/path/to/component.ontology",
"/path/to/function.ontology",
"/path/to/process.ontology"] );
Function: Creates a new dagflat parser.
Returns : A new dagflat parser object, implementing Bio::OntologyIO.
Args : -defs_file => the name of the file holding the term
definitions
-files => a single ontology flat file holding the
term relationships, or an array ref holding
the file names (for GO, there will usually be
3 files: component.ontology, function.ontology,
process.ontology)
-file => if there is only a single flat file, it may
also be specified via the -file parameter
-ontology_name => the name of the ontology; if not specified the
parser will auto-discover it by using the term
that starts with a $, and converting underscores
to spaces
-engine => the Bio::Ontology::OntologyEngineI object
to be reused (will be created otherwise); note
that every Bio::Ontology::OntologyI will
qualify as well since that one inherits from the
former.
See L<Bio::OntologyIO>.
=cut
# in reality, we let OntologyIO::new do the instantiation, and override
# _initialize for all initialization work
sub _initialize {
my ($self, %arg) = @_;
my ( $defs_file_name,$files,$defs_url,$url,$name,$eng ) =
$self->_rearrange([qw( DEFS_FILE
FILES
DEFS_URL
URL
ONTOLOGY_NAME
ENGINE)
],
%arg );
delete($arg{-url}); #b/c GO has 3 files...
$self->SUPER::_initialize( %arg );
$self->_done( FALSE );
$self->_not_first_record( FALSE );
$self->_term( "" );
delete $self->{'_ontologies'};
# ontology engine (and possibly name if it's an OntologyI)
$eng = Bio::Ontology::OBOEngine->new() unless $eng;
if($eng->isa("Bio::Ontology::OntologyI")) {
$self->ontology_name($eng->name());
$eng = $eng->engine() if $eng->can('engine');
}
$self->_ont_engine($eng);
# flat files to parse
if(defined($defs_file_name) && defined($defs_url)){
$self->throw('cannot provide both -defs_file and -defs_url');
} else {
defined($defs_file_name) && $self->defs_file( $defs_file_name );
defined($defs_url) && $self->defs_url( $defs_url );
}
if(defined($files) && defined($url)){
} elsif(defined($files)){
$self->{_flat_files} = $files ? ref($files) ? $files : [$files] : [];
} elsif(defined($url)){
$self->url($url);
}
# ontology name (overrides implicit one through OntologyI engine)
$self->ontology_name($name) if $name;
} # _initialize
=head2 ontology_name
Title : ontology_name
Usage : $obj->ontology_name($newval)
Function: Get/set the name of the ontology parsed by this module.
Example :
Returns : value of ontology_name (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub ontology_name{
my $self = shift;
return $self->{'ontology_name'} = shift if @_;
return $self->{'ontology_name'};
}
=head2 parse
Title : parse()
Usage : $parser->parse();
Function: Parses the files set with "new" or with methods
defs_file and _flat_files.
Normally you should not need to call this method as it will
be called automatically upon the first call to
next_ontology().
Returns : [Bio::Ontology::OntologyEngineI]
Args :
=cut
sub parse {
my $self = shift;
#warn "PARSING";
# setup the default term factory if not done by anyone yet
$self->term_factory(Bio::Ontology::TermFactory->new(
-type => "Bio::Ontology::Term"))
unless $self->term_factory();
# create the ontology object itself
my $ont = Bio::Ontology::Ontology->new(-name => $self->ontology_name(),
-engine => $self->_ont_engine());
# parse definitions
while( my $term = $self->_next_term() ) {
$self->_add_term( $term, $ont );
}
# set up the ontology of the relationship types
foreach ($self->_part_of_relationship(), $self->_is_a_relationship(), $self->_related_to_relationship()) {
$_->ontology($ont);
}
# pre-seed the IO system with the first flat file if -file wasn't provided
if(! $self->_fh) {
if($self->url){
if(ref($self->url) eq 'ARRAY'){
#warn "BA";
foreach my $url (@{ $self->url }){
#warn $url;
#warn $ont;
#warn scalar($ont->get_all_terms());
$self->_initialize_io(-url => $url);
$self->_parse_flat_file($ont);
}
$self->close();
} else {
$self->_initialize_io(-url => $self->url);
}
} elsif($self->_flat_files){
$self->_initialize_io(-file => shift(@{$self->_flat_files()}));
}
}
while($self->_fh) {
$self->_parse_flat_file($ont);
# advance to next flat file if more are available
if(@{$self->_flat_files()}) {
$self->close();
$self->_initialize_io(-file => shift(@{$self->_flat_files()}));
} else {
last; # nothing else to parse so terminate the loop
}
}
$self->_add_ontology($ont);
# not needed anywhere, only because of backward compatibility
return $self->_ont_engine();
} # parse
=head2 next_ontology
Title : next_ontology
Usage :
Function: Get the next available ontology from the parser. This is the
method prescribed by Bio::OntologyIO.
Example :
Returns : An object implementing Bio::Ontology::OntologyI, and undef if
there is no more ontology in the input.
Args :
=cut
sub next_ontology {
my $self = shift;
# parse if not done already
$self->parse() unless exists($self->{'_ontologies'});
# return next available ontology
if(exists($self->{'_ontologies'})){
my $ont = shift (@{$self->{'_ontologies'}});
if($ont){
my $store = Bio::Ontology::OntologyStore->new();
$store->register_ontology($ont);
return $ont;
}
}
return;
}
=head2 defs_file
Title : defs_file
Usage : $parser->defs_file( "GO.defs" );
Function: Set/get for the term definitions filename.
Returns : The term definitions file name [string].
Args : On set, the term definitions file name [string] (optional).
=cut
sub defs_file {
my $self = shift;
if ( @_ ) {
my $f = shift;
$self->{ "_defs_file_name" } = $f;
$self->_defs_io->close() if $self->_defs_io();
if(defined($f)) {
$self->_defs_io( Bio::Root::IO->new( -input => $f ) );
}
}
return $self->{ "_defs_file_name" };
} # defs_file
sub defs_url {
my $self = shift;
my $val = shift;
if(defined($val)){
$self->{'_defs_url'} = $val;
$self->_defs_io->close() if $self->_defs_io();
$self->_defs_io( Bio::Root::IO->new( -url => $val ) );
}
return $self->{'_defs_url'};
}
sub url {
my $self = shift;
my $val = shift;
if(defined($val)){
$self->{'_url'} = $val;
}
return $self->{'_url'};
}
=head2 close
Title : close
Usage :
Function: Closes this ontology stream and associated file handles.
Clients should call this method especially when they write
ontologies.
We need to override this here in order to close the file
handle for the term definitions file.
Example :
Returns : none
Args : none
=cut
sub close{
my $self = shift;
# first call the inherited implementation
$self->SUPER::close();
# then close the defs file io (if there is one)
$self->_defs_io->close() if $self->_defs_io();
}
=head2 _flat_files
Title : _flat_files
Usage : $files_to_parse = $parser->_flat_files();
Function: Get the array of ontology flat files that need to be parsed.
Note that this array will decrease in elements over the
parsing process. Therefore, it\'s value outside of this
module will be limited. Also, be careful not to alter the
array unless you know what you are doing.
Returns : a reference to an array of zero or more strings
Args : none
=cut
sub _flat_files {
my $self = shift;
$self->{_flat_files} = [] unless exists($self->{_flat_files});
return $self->{_flat_files};
}
# INTERNAL METHODS
# ----------------
=head2 _defs_io
Title : _defs_io
Usage : $obj->_defs_io($newval)
Function: Get/set the Bio::Root::IO instance representing the
definition file, if provided (see defs_file()).
Example :
Returns : value of _defs_io (a Bio::Root::IO object)
Args : on set, new value (a Bio::Root::IO object or undef, optional)
=cut
sub _defs_io{
my $self = shift;
return $self->{'_defs_io'} = shift if @_;
return $self->{'_defs_io'};
}
sub _add_ontology {
my $self = shift;
$self->{'_ontologies'} = [] unless exists($self->{'_ontologies'});
foreach my $ont (@_) {
$self->throw(ref($ont)." does not implement Bio::Ontology::OntologyI")
unless ref($ont) && $ont->isa("Bio::Ontology::OntologyI");
# the ontology name may have been auto-discovered while parsing
# the file
$ont->name($self->ontology_name) unless $ont->name();
push(@{$self->{'_ontologies'}}, $ont);
}
}
# This simply delegates. See SimpleGOEngine.
sub _add_term {
my ( $self, $term, $ont ) = @_;
$term->ontology($ont) if $ont && (! $term->ontology);
$self->_ont_engine()->add_term( $term );
} # _add_term
# This simply delegates. See SimpleGOEngine
sub _part_of_relationship {
my $self = shift;
return $self->_ont_engine()->part_of_relationship(@_);
} # _part_of_relationship
# This simply delegates. See SimpleGOEngine
sub _is_a_relationship {
my $self = shift;
return $self->_ont_engine()->is_a_relationship(@_);
} # _is_a_relationship
# This simply delegates. See SimpleGOEngine
sub _related_to_relationship {
my $self = shift;
return $self->_ont_engine()->related_to_relationship(@_);
} # _is_a_relationship
# This simply delegates. See SimpleGOEngine
sub _add_relationship {
my ( $self, $parent, $child, $type, $ont ) = @_;
# note the triple terminology (subject,predicate,object) corresponds to
# (child,type,parent)
$self->_ont_engine()->add_relationship( $child, $type, $parent, $ont );
} # _add_relationship
# This simply delegates. See SimpleGOEngine
sub _has_term {
my $self = shift;
return $self->_ont_engine()->has_term( @_ );
} # _add_term
# This parses the relationships files
sub _parse_flat_file {
my $self = shift;
my $ont = shift;
my @stack = ();
my $prev_spaces = -1;
my $prev_term = "";
while ( my $line = $self->_readline() ) {
if ( $line =~ /^!/ ) {
next;
}
# split into term specifications
my @termspecs = split(/ (?=[%<])/, $line);
# the first element is whitespace only
shift(@termspecs) if $termspecs[0] =~ /^\s*$/;
# parse out the focus term
my $current_term = $self->_get_first_termid( $termspecs[0] );
my @syns = $self->_get_synonyms( $termspecs[0] );
my @sec_go_ids = $self->_get_secondary_termids( $termspecs[0] );
my @cross = $self->_get_db_cross_refs( $termspecs[0] );
my @cross_refs;
foreach my $cross_ref (@cross) {
$cross_ref eq $current_term && next;
push(@cross_refs, $cross_ref);
}
# parse out the parents of the focus term
shift(@termspecs);
my @isa_parents = ();
my @partof_parents = ();
foreach my $parent (@termspecs) {
if (index($parent, "%") == 0) {
push(@isa_parents, $self->_get_first_termid($parent));
} elsif (index($parent, "<") == 0) {
push(@partof_parents, $self->_get_first_termid($parent));
} else {
$self->warn("unhandled relationship type in '".$parent."'");
}
}
if ( ! $self->_has_term( $current_term ) ) {
my $term =$self->_create_ont_entry($self->_get_name($line,
$current_term),
$current_term );
$self->_add_term( $term, $ont );
}
my $current_term_object = $self->_ont_engine()->get_terms( $current_term );
my $anno = $self->_to_annotation(\@cross_refs);
$current_term_object->add_dbxref(-dbxrefs => $anno);
$current_term_object->add_secondary_id( @sec_go_ids );
$current_term_object->add_synonym( @syns );
unless ( $line =~ /^\$/ ) {
$current_term_object->ontology( $ont );
}
foreach my $parent ( @isa_parents ) {
if ( ! $self->_has_term( $parent ) ) {
my $term = $self->_create_ont_entry($self->_get_name($line,
$parent),
$parent );
$self->_add_term( $term, $ont );
}
$self->_add_relationship( $parent,
$current_term,
$self->_is_a_relationship(),
$ont);
}
foreach my $parent ( @partof_parents ) {
if ( ! $self->_has_term( $parent ) ) {
my $term = $self->_create_ont_entry($self->_get_name($line,
$parent),
$parent );
$self->_add_term( $term, $ont );
}
$self->_add_relationship( $parent,
$current_term,
$self->_part_of_relationship(),
$ont);
}
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 {
$self->throw( "format error (file ".$self->file.")" );
}
}
my $parent = $stack[ @stack - 1 ];
# add a relationship if the line isn\'t the one with the root term
# of the ontology (which is also the name of the ontology)
if ( index($line,'$') != 0 ) {
#adding @reltype@ syntax
if ( $line !~ /^\s*([<%~]|\@\w+?\@)/ ) {
$self->throw( "format error (file ".$self->file.") offending line:\n$line" );
}
my($relstring) = $line =~ /^\s*([<%~]|\@[^\@]+?\@)/;
my $reltype;
if ($relstring eq '<') {
$reltype = $self->_part_of_relationship;
} elsif ($relstring eq '%') {
$reltype = $self->_is_a_relationship;
} elsif ($relstring eq '~') {
$reltype = $self->_related_to_relationship;
} else {
$relstring =~ s/\@//g;
if ($self->_ont_engine->get_relationship_type($relstring)) {
$reltype = $self->_ont_engine->get_relationship_type($relstring);
} else {
$self->_ont_engine->add_relationship_type($relstring, $ont);
$reltype = $self->_ont_engine->get_relationship_type($relstring);
}
}
#my $reltype = ($line =~ /^\s*</) ?
#$self->_part_of_relationship() :
#$self->_is_a_relationship();
$self->_add_relationship( $parent, $current_term, $reltype, $ont);
}
$prev_spaces = $current_spaces;
$prev_term = $current_term;
}
return $ont;
} # _parse_relationships_file
# Parses the 1st term id number out of line.
sub _get_first_termid {
my ( $self, $line ) = @_;
if ( $line =~ /;\s*([A-Z_]{1,8}:\d{1,})/ ) {
# if ( $line =~ /;\s*(\w+:\w+)/ ) {
return $1;
}
else {
$self->throw( "format error: no term id in line \"$line\"" );
}
} # _get_first_termid
# Parses the name out of line.
sub _get_name {
my ( $self, $line, $termid ) = @_;
if ( $line =~ /([^;<%~]+);\s*$termid/ ) {
my $name = $1;
# remove trailing and leading whitespace
$name =~ s/\s+$//;
$name =~ s/^\s+//;
$name =~ s/\@.+?\@//;
# remove leading dollar character; also we default the name of the
# ontology to this name unless it is preset to something else
if(index($name,'$') == 0) {
$name = substr($name,1);
# replace underscores by spaces for setting the ontology name
$self->ontology_name(join(" ",split(/_/,$name)))
unless $self->ontology_name();
}
return $name;
}
else {
return;
}
} # _get_name
# Parses the synonyms out of line.
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
# Parses the db cross refs out of line.
sub _get_db_cross_refs {
my ( $self, $line ) = @_;
my @refs = ();
while ( $line =~ /;([^;<%~:]+:[^;<%~:]+)/g ) {
my $ref = $1;
if ( $ref =~ /synonym/ || $ref =~ /[A-Z]{1,8}:\d{3,}/ ) {
next;
}
$ref =~ s/\s+$//;
$ref =~ s/^\s+//;
$ref = $self->unescape( $ref );
push( @refs, $ref ) if defined $ref;
}
return @refs;
}
# Parses the secondary go ids out of a line
sub _get_secondary_termids {
my ( $self, $line ) = @_;
my @secs = ();
# while ( $line =~ /,\s*([A-Z]{1,8}:\d{3,})/g ) {
while ( $line =~ /,\s*(\w+:\w+)/g ) {
my $sec = $1;
push( @secs, $sec );
}
return @secs;
} # _get_secondary_termids
# Counts the spaces at the beginning of a line in the relationships files
sub _count_spaces {
my ( $self, $line ) = @_;
if ( $line =~ /^(\s+)/ ) {
return length( $1 );
}
else {
return 0;
}
} # _count_spaces
# "next" method for parsing the defintions file
sub _next_term {
my ( $self ) = @_;
if ( ($self->_done() == TRUE) || (! $self->_defs_io())) {
return;
}
my $line = "";
my $termid = "";
my $next_term = $self->_term();
my $def = "";
my $comment = "";
my @def_refs = ();
my $isobsolete;
while( $line = ( $self->_defs_io->_readline() ) ) {
if ( $line !~ /\S/
|| $line =~ /^\s*!/ ) {
next;
}
elsif ( $line =~ /^\s*term:\s*(.+)/ ) {
$self->_term( $1 );
last if $self->_not_first_record();
$next_term = $1;
$self->_not_first_record( TRUE );
}
elsif ( $line =~ /^\s*[a-z]{0,8}id:\s*(.+)/ ) {
$termid = $1;
}
elsif ( $line =~ /^\s*definition:\s*(.+)/ ) {
$def = $self->unescape($1);
$isobsolete = 1 if index($def,"OBSOLETE") == 0;
}
elsif ( $line =~ /^\s*definition_reference:\s*(.+)/ ) {
push( @def_refs, $self->unescape($1) );
}
elsif ( $line =~ /^\s*comment:\s*(.+)/ ) {
$comment = $self->unescape($1);
}
}
$self->_done( TRUE ) unless $line; # we'll come back until done
return $self->_create_ont_entry( $next_term, $termid, $def,
$comment, \@def_refs, $isobsolete);
} # _next_term
# Holds the GO engine to be parsed into
sub _ont_engine {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_ont_engine" } = $value;
}
return $self->{ "_ont_engine" };
} # _ont_engine
# Used to create ontology terms.
# Arguments: name, id
sub _create_ont_entry {
my ( $self, $name, $termid, $def, $cmt, $dbxrefs, $obsolete ) = @_;
if((!defined($obsolete)) && (index(lc($name),"obsolete") == 0)) {
$obsolete = 1;
}
my $anno = $self->_to_annotation($dbxrefs);
my $term = $self->term_factory->create_object(-name => $name,
-identifier => $termid,
-definition => $def,
-comment => $cmt,
-dbxrefs => $anno,
-is_obsolete => $obsolete);
return $term;
} # _create_ont_entry
# Holds whether first record or not
sub _not_first_record {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_not_first_record" } = $value;
}
return $self->{ "_not_first_record" };
} # _not_first_record
# Holds whether done or not
sub _done {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_done" } = $value;
}
return $self->{ "_done" };
} # _done
# Holds a term.
sub _term {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_term" } = $value;
}
return $self->{ "_term" };
} # _term
# convert simple strings to Bio::Annotation::DBLinks
sub _to_annotation {
my ($self , $links) = @_;
return unless $links;
my @dbxrefs;
for my $string (@{$links}) {
my ($db, $id) = split(':',$string);
push @dbxrefs, Bio::Annotation::DBLink->new(-database => $db, -primary_id => $id);
}
return \@dbxrefs;
}
1;