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

Support¶

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 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://github.com/bioperl/bioperl-live/issues

CONTRIBUTOR¶

Christian Zmasek

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 one to parse multiple input
                             files into the same ontology and still have
                             separately rooted.
           -engine        => the L<Bio::Ontology::OntologyEngineI> object
                             to be reused (will be created otherwise); note
                             that every L<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.

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)

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    :

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    :

_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

_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)

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)

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 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_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)