# $Id: simplehierarchy.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::OntologyIO::simplehierarchy # # Please direct questions and support issues to # # Cared for by Allen Day, allenday@ucla.edu # # (c) Allen Day, allenday@ucla.edu, 2003. # (c) Department of Human Genetics, UCLA Medical School, 2003. # # 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::simplehierarchy - a base class parser for simple hierarchy-by-indentation type formats =head1 SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "simplehierarchy", -file => "pathology_terms.csv", -indent_string => ",", -ontology_name => "eVOC", -term_factory => $fact, ); my $ontology = $parser->next_ontology(); =head1 DESCRIPTION Needs Graph.pm from CPAN. This class is nearly identical to OntologyIO::dagflat, see L for details. =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 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: http://bugzilla.open-bio.org/ =head1 AUTHOR Allen Day Email: allenday@ucla.edu =head2 CONTRIBUTOR Christian Zmasek =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::simplehierarchy; use strict; use Data::Dumper; use File::Basename; use Bio::Root::IO; use Bio::Ontology::OBOEngine; use Bio::Ontology::Ontology; use Bio::Ontology::TermFactory; use constant TRUE => 1; use constant FALSE => 0; use base qw(Bio::OntologyIO); =head2 new Title : new Usage : see SYNOPSIS Function: Creates a new simplehierarchy parser. Returns : A new simplehierarchy parser object, implementing Bio::OntologyIO. Args : -files => a single ontology flat file holding the term relationships, or an array ref holding the file names -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, defaults to "Gene Ontology" -file_is_root => Boolean indicating whether a virtual root term is to be added, the name of which will be derived from the file name. Default is false. Enabling this allows to parse multiple input files into the same ontology and still have separately rooted. -engine => the L object to be reused (will be created otherwise); note that every L will qualify as well since that one inherits from the former. -indent_string => the string used to indent hierarchical levels in the file. For a file like this: term0 subterm1A subterm2A subterm1B subterm1C indent_string would be " ". Defaults to one space (" "). -comment_char => Allows specification of a regular expression string to indicate a comment line. Currently defaults to "[\|\-]". Note: this is not yet implemented. See L. =cut # in reality, we let OntologyIO::new do the instantiation, and override # _initialize for all initialization work sub _initialize { my ($self, @args) = @_; $self->SUPER::_initialize( @args ); my ( $indent,$files,$fileisroot,$name,$eng ) = $self->_rearrange([qw(INDENT_STRING FILES FILE_IS_ROOT ONTOLOGY_NAME ENGINE) ], @args); $self->_done( FALSE ); $self->_not_first_record( FALSE ); $self->_term( "" ); $self->file_is_root($fileisroot) if defined($fileisroot); $indent = ' ' unless defined($indent); #reasonable default? # the indentation string may have escaped chars if (($indent =~ /\\/) && ($indent !~ /[\$\`]/)) { $indent = "\$indent = \"$indent\""; eval $indent; } $self->indent_string($indent); 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 $self->{_flat_files} = $files ? ref($files) ? $files : [$files] : []; # 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; # 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 => $self->_ont_engine()); # set up the ontology of the relationship types foreach ($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) { $self->_initialize_io(-file => shift(@{$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(); # reset the virtual root so that the next one is generated from # the next file $self->_virtual_root(undef); # now re-initialize the IO object $self->_initialize_io(-file => shift(@{$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 return shift(@{$self->{'_ontologies'}}) if exists($self->{'_ontologies'}); return; } =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) && $ont->isa("Bio::Ontology::OntologyI"); push(@{$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, $term ) = @_; return $self->_ont_engine()->part_of_relationship(); } # _part_of_relationship # This simply delegates. See SimpleGOEngine sub _is_a_relationship { my ( $self, $term ) = @_; return $self->_ont_engine()->is_a_relationship(); } # _is_a_relationship # This simply delegates. See SimpleGOEngine sub _related_to_relationship { my ( $self, $term ) = @_; 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, $term ) = @_; $term = $self->ontology_name() .'|'. $term unless ref($term) || !$self->ontology_name(); return $self->_ont_engine()->has_term( $term ); } # _add_term # This simply delegates after prefixing the namespace name if it is just a # base identifier. See SimpleGOEngine sub _get_terms{ my $self = shift; my @args = (); while(@_) { unshift(@args, pop(@_)); # this actually does preserve the order $args[0] = $self->ontology_name() .'|'. $args[0] unless ref($args[0]) || !$self->ontology_name(); } return $self->_ont_engine->get_terms(@args); } # This parses the relationships files sub _parse_flat_file { my $self = shift; my $ont = shift; my @stack = (); my $prev_indent = -1; my $parent = ""; my $prev_term = ""; my $indent_string = $self->indent_string; while ( my $line = $self->_readline() ) { if ( $line =~ /^[$indent_string]*[\|\-]/ ) { #this is not yet generalized next; } my ($current_term) = $line =~ /^[$indent_string]*(.*)/; my $current_indent = $self->_count_indents( $line ); chomp $current_term; # remove extraneous delimiter characters at the end of the name if any $current_term =~ s/[$indent_string]+$//; # remove double quotes surrounding the entry, if any $current_term =~ s/^\"(.*)\"$/$1/; # also, the name might contain a synonym my $syn = $current_term =~ s/\s+{([^}]+)}// ? $1 : undef; if ( ! $self->_has_term( $current_term ) ) { my $term = $self->_create_ont_entry($current_term); # add synonym(s) if any $term->add_synonym(split(/[;,]\s*/,$syn)) if $syn; # add to the machine $self->_add_term( $term, $ont ); #go on to the next term if a root node. if($current_indent == 0) { # add the virtual root as parent if there is one if($self->_virtual_root()) { $self->_add_relationship($self->_virtual_root(), $term, $self->_is_a_relationship(), $ont); } $prev_indent = $current_indent; $prev_term = $current_term; push @stack, $current_term; next; } } # note: we are ensured to see the parent first in this type of file, # so we never need to possibly insert the parent here if ( $current_indent != $prev_indent ) { if ( $current_indent == $prev_indent + 1 ) { push( @stack, $prev_term ); } elsif ( $current_indent < $prev_indent ) { my $n = $prev_indent - $current_indent; for ( my $i = 0; $i < $n; ++$i ) { pop( @stack ); } } else { $self->throw("format error: indentation level $current_indent " ."is more than one higher than the previous " ."level $prev_indent ('$current_term', " ."file ".$self->file.")" ); } } $parent = $stack[-1]; if($parent ne $current_term) { #this prevents infinite recursion from a parent linking to itself $self->_add_relationship($self->_get_terms($parent), $self->_get_terms($current_term), $self->_is_a_relationship(), $ont); } $prev_indent = $current_indent; $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{7})/ ) { return $1; } else { $self->throw( "format error: no term id in line \"$line\"" ); } } # _get_first_termid # Counts the indents at the beginning of a line in the relationships files sub _count_indents { my ( $self, $line ) = @_; my $indent = $self->indent_string; if ( $line =~ /^($indent+)/ ) { return (length($1)/length($indent)); } else { return 0; } } # _count_indents # 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 ) = @_; my $term = $self->term_factory->create_object(-name => $name, -identifier => $termid); return $term; } # _create_ont_entry # Holds whether first record or not 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 # Holds whether done or not 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 # Holds a term. sub _term { my ( $self, $value ) = @_; if ( defined $value ) { $self->{ "_term" } = $value; } return $self->{ "_term" }; } # _term =head2 indent_string Title : indent_string Usage : $obj->indent_string($newval) Function: Example : Returns : value of indent_string (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub indent_string{ my $self = shift; return $self->{'indent_string'} = shift if @_; return $self->{'indent_string'}; } =head2 file_is_root Title : file_is_root Usage : $obj->file_is_root($newval) Function: Boolean indicating whether a virtual root term is to be added, the name of which will be derived from the file name. Enabling this allows to parse multiple input files into the same ontology and still have separately rooted. Example : Returns : value of file_is_root (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub file_is_root{ my $self = shift; return $self->{'file_is_root'} = shift if @_; return $self->{'file_is_root'}; } =head2 _virtual_root Title : _virtual_root Usage : $obj->_virtual_root($newval) Function: Example : Returns : value of _virtual_root (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub _virtual_root{ my $self = shift; return $self->{'_virtual_root'} = shift if @_; # don't return anything if not in file_is_root mode, or if we don't # have a file to derive the root node from return unless $self->file_is_root() && $self->file(); # construct it if we haven't done this before if(! $self->{'_virtual_root'}) { my ($rt,undef,undef) = fileparse($self->file(), '\..*'); $rt =~ s/_/ /g; $rt = $self->_create_ont_entry($rt); $self->_add_term($rt, $self->ontology_name()); $self->{'_virtual_root'} = $rt; } return $self->{'_virtual_root'}; } 1;