Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/Factory/SeqAnalysisParserFactory.pm @ 0:1f6dce3d34e0
Uploaded
author | mahtabm |
---|---|
date | Thu, 11 Apr 2013 02:01:53 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/Factory/SeqAnalysisParserFactory.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,167 @@ +# $Id: SeqAnalysisParserFactory.pm,v 1.9 2002/12/01 00:05:20 jason Exp $ +# +# BioPerl module for Bio::Factory::SeqAnalysisParserFactory +# +# Cared for by Jason Stajich <jason@bioperl.org>, +# and Hilmar Lapp <hlapp@gmx.net> +# +# Copyright Jason Stajich, Hilmar Lapp +# +# You may distribute this module under the same terms as perl itself + +# POD documentation - main docs before the code + +=head1 NAME + +Bio::Factory::SeqAnalysisParserFactory - class capable of + creating SeqAnalysisParserI compliant parsers + +=head1 SYNOPSIS + + # 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); + } + +=head1 DESCRIPTION + +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). + +=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 one of the Bioperl mailing lists. +Your participation is much appreciated. + + bioperl-l@bioperl.org - General discussion + http://bio.perl.org/MailList.html - About the mailing lists + +=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 email or the web: + + bioperl-bugs@bio.perl.org + http://bugzilla.bioperl.org/ + +=head1 AUTHOR - Hilmar Lapp, Jason Stajich + +Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt> + +=head1 APPENDIX + +The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ + +=cut + +package Bio::Factory::SeqAnalysisParserFactory; +use strict; + +use Bio::Factory::SeqAnalysisParserFactoryI; +use Bio::Factory::DriverFactory; + +use vars qw(@ISA); +@ISA = qw(Bio::Factory::DriverFactory Bio::Factory::SeqAnalysisParserFactoryI); + +BEGIN { + Bio::Factory::DriverFactory->register_driver + ( + "genscan" => "Bio::Tools::Genscan", + "mzef" => "Bio::Tools::MZEF", + "estscan" => "Bio::Tools::ESTScan", + "bplite" => "Bio::Tools::BPlite", + "blast" => "Bio::Tools::BPlite", + "hmmer" => "Bio::Tools::HMMER::Result", + "gff" => "Bio::Tools::GFF", + "sim4" => "Bio::Tools::Sim4::Results", + "epcr" => "Bio::Tools::EPCR", + "exonerate" => "Bio::Tools::Exonerate", + ); +} + +sub new { + my ($class, @args) = @_; + my $self = $class->SUPER::new(@args); + + # no per-object initialization right now - registration of default drivers + # is only done once when the module is loaded + return $self; +} + +=head2 get_parser + + Title : get_parser + Usage : $factory->get_parser(-input=>$inputobj, + [ -params=>[@params] ], + -method => $method) + Function: Creates and returns a parser object for the given input and method. + Both file names and streams (filehandles) are allowed. + + Parameters (-params argument) are passed on to the parser object + and therefore are specific to the parser to be created. + Example : + Returns : A Bio::SeqAnalysisParserI implementing object. Exception if + creation of the parser object fails. + Args : B<input> - object/file where analysis results are coming from, + B<params> - parameter to use when parsing/running analysis + B<method> - method of analysis + +=cut + +sub get_parser { + my ($self, @args) = @_; + my $parser; + my $module; + + my ($input, $params, $method) = + $self->_rearrange([qw(INPUT PARAMS METHOD)], @args); + + # retrieve module name for requested method + $method = lc $method; # method is case-insensitive + $module = $self->get_driver($method); + if(! defined($module)) { + $self->throw("Analysis parser driver for method $method not registered."); + } + # load module + $self->_load_module($module); # throws an exception on failure to load + # make sure parameters is not undef + $params = [] if( !defined $params ); + # figure out input method (file or stream) + my $inputmethod = '-file'; + if( ref($input) =~ /GLOB/i ) { + $inputmethod = '-fh'; + } + # instantiate parser and return the result + $parser = $module->new($inputmethod => $input, @$params); + if(! $parser->isa('Bio::SeqAnalysisParserI')) { + $self->throw("Driver $module registered for method $method does not implement Bio::SeqAnalyisParserI. How come?"); + } + return $parser; +} + +1;