| Bio::Factory::SeqAnalysisParserFactory(3pm) | User Contributed Perl Documentation | Bio::Factory::SeqAnalysisParserFactory(3pm) |
Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers
# initialize an object implementing this interface, e.g.
$factory = Bio::Factory::SeqAnalysisParserFactory->new();
# find out the methods it knows about
print "registered methods: ",
join(', ', keys %{$factory->driver_table}), "\n";
# obtain a parser object
$parser = $factory->get_parser(-input=>$inputobj,
-params=>[@params],
-method => $method);
# $parser is an object implementing Bio::SeqAnalysisParserI
# annotate sequence with features produced by parser
while(my $feat = $parser->next_feature()) {
$seq->add_SeqFeature($feat);
}
This is a factory class capable of instantiating SeqAnalysisParserI implementing parsers.
The concept behind this class and the interface it implements (Bio::Factory::SeqAnalysisParserFactoryI) is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See Bio::SeqAnalysisParserI for more documentation of this concept.
You can always find out the methods an instance of this class knows about by the way given in the SYNOPSIS section. By default, and assuming that the documentation is up-to-date, this will comprise of genscan, mzef, estscan, blast, hmmer, gff, and sim4 (all case-insensitive).
User feedback is an integral part of the evolution of this and
other Bioperl modules. Send your comments and suggestions preferably
to one of 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
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.
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
Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_parser
Usage : $factory->get_parser(-input=>$inputobj,
[ -params=>[@params] ],
-method => $method)
Function: Creates and returns a parser object for the given input and method.
Both file names and streams (filehandles) are allowed.
Parameters (-params argument) are passed on to the parser object
and therefore are specific to the parser to be created.
Example :
Returns : A Bio::SeqAnalysisParserI implementing object. Exception if
creation of the parser object fails.
Args : B<input> - object/file where analysis results are coming from,
B<params> - parameter to use when parsing/running analysis
B<method> - method of analysis
Title : register_driver
Usage : $factory->register_driver("genscan", "Bio::Tools::Genscan");
Function: Registers a driver a factory class should be able to instantiate.
This method can be called both as an instance and as a
class method.
Returns :
Args : Key of the driver (string) and the module implementing the driver
(string).
Title : driver_table
Usage : $table = $factory->driver_table();
Function: Returns a reference to the hash table storing associations of
methods with drivers.
You use this table to look up registered methods (keys) and
drivers (values).
In this implementation the table is class-specific and
therefore shared by all instances. You can override this in
a derived class, but note that this method can be called
both as an instance and a class method.
This will be the table used by the object internally. You
should definitely know what you're doing if you modify the
table's contents. Modifications are shared by _all_
instances, those present and those yet to be created.
Returns : A reference to a hash table.
Args :
| 2021-08-15 | perl v5.32.1 |