Bio::OntologyIO simplehierarchy
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Summary
Bio::OntologyIO::simplehierarchy - a base class parser for simple hierarchy-by-indentation
type formats
Package variables
No package variables defined.
Included modules
Bio::Ontology::OBOEngine
Bio::Ontology::Ontology
Bio::Ontology::TermFactory
Bio::Root::IO
Data::Dumper
File::Basename
Inherit
Bio::OntologyIO
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();
Description
Needs Graph.pm from CPAN. This class is nearly identical to
OntologyIO::dagflat, see Bio::OntologyIO::dagflat for details.
Methods
_initialize
No description
Code
ontology_nameDescriptionCode
parseDescriptionCode
next_ontologyDescriptionCode
_flat_filesDescriptionCode
_defs_ioDescriptionCode
_add_ontology
No description
Code
_add_term
No description
Code
_part_of_relationship
No description
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_is_a_relationship
No description
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_related_to_relationship
No description
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_add_relationship
No description
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_has_term
No description
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_get_terms
No description
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_parse_flat_file
No description
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_get_first_termid
No description
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_count_indents
No description
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_ont_engine
No description
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_create_ont_entry
No description
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_not_first_record
No description
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_done
No description
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_term
No description
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indent_stringDescriptionCode
file_is_rootDescriptionCode
_virtual_rootDescriptionCode
Methods description
ontology_namecode    nextTop
 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)
parsecodeprevnextTop
 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 :
next_ontologycodeprevnextTop
 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 :
_flat_filescodeprevnextTop
 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
_defs_iocodeprevnextTop
 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)
indent_stringcodeprevnextTop
 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)
file_is_rootcodeprevnextTop
 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 one 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)
_virtual_rootcodeprevnextTop
 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)
Methods code
_initializedescriptionprevnextTop
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
}
ontology_namedescriptionprevnextTop
sub ontology_name {
    my $self = shift;

    return $self->{'ontology_name'} = shift if @_;
    return $self->{'ontology_name'};
}
parsedescriptionprevnextTop
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
}
next_ontologydescriptionprevnextTop
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;
}
_flat_filesdescriptionprevnextTop
sub _flat_files {
    my $self = shift;

    $self->{_flat_files} = [] unless exists($self->{_flat_files});
    return $self->{_flat_files};
}


# INTERNAL METHODS
# ----------------
}
_defs_iodescriptionprevnextTop
sub _defs_io {
    my $self = shift;

    return $self->{'_defs_io'} = shift if @_;
    return $self->{'_defs_io'};
}
_add_ontologydescriptionprevnextTop
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.
}
_add_termdescriptionprevnextTop
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
}
_part_of_relationshipdescriptionprevnextTop
sub _part_of_relationship {
    my ( $self, $term ) = @_;

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

} # _part_of_relationship
# This simply delegates. See SimpleGOEngine
}
_is_a_relationshipdescriptionprevnextTop
sub _is_a_relationship {
    my ( $self, $term ) = @_;

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

} # _is_a_relationship
# This simply delegates. See SimpleGOEngine
}
_related_to_relationshipdescriptionprevnextTop
sub _related_to_relationship {
    my ( $self, $term ) = @_;

    return $self->_ont_engine()->related_to_relationship();

} # _is_a_relationship
# This simply delegates. See SimpleGOEngine
}
_add_relationshipdescriptionprevnextTop
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
}
_has_termdescriptionprevnextTop
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
}
_get_termsdescriptionprevnextTop
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
}
_parse_flat_filedescriptionprevnextTop
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.
}
_get_first_termiddescriptionprevnextTop
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
}
_count_indentsdescriptionprevnextTop
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
}
_ont_enginedescriptionprevnextTop
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
}
_create_ont_entrydescriptionprevnextTop
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
}
_not_first_recorddescriptionprevnextTop
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
}
_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
# Holds a term.
}
_termdescriptionprevnextTop
sub _term {
    my ( $self, $value ) = @_;

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

    return $self->{ "_term" };
} # _term
}
indent_stringdescriptionprevnextTop
sub indent_string {
    my $self = shift;

    return $self->{'indent_string'} = shift if @_;
    return $self->{'indent_string'};
}
file_is_rootdescriptionprevnextTop
sub file_is_root {
    my $self = shift;

    return $self->{'file_is_root'} = shift if @_;
    return $self->{'file_is_root'};
}
_virtual_rootdescriptionprevnextTop
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;
}
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
SupportTop
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
Allen Day
Email: allenday@ucla.edu
CONTRIBUTORTop
Christian Zmasek
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
newTop
 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 one to parse multiple input
files into the same ontology and still have
separately rooted.
-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.
-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 Bio::OntologyIO.