Bio::OntologyIO::simplUserrContributed PerlBio::OntologyIO::simplehierarchy(3)NAMEBio::OntologyIO::simplehierarchy - a base class parser for simple
hierarchy-by-indentation
type formats
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.
FEEDBACK
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:
http://bugzilla.open-bio.org/
AUTHOR
Allen Day
Email: allenday@ucla.edu
CONTRIBUTOR
Christian Zmasek
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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<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 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)
perl v5.14.12011-07-2Bio::OntologyIO::simplehierarchy(3)
